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<!doctype html><html lang=en class=no-js><head><meta charset=utf-8><meta name=viewport content="width=device-width,initial-scale=1,shrink-to-fit=no"><meta name=generator content="Hugo 0.81.0"><meta name=ROBOTS content="INDEX, FOLLOW NOARCHIVE"><title>NCBI Genomes FTP</title><meta property="og:title" content="NCBI Genomes FTP"><meta property="og:description" content="The Genomes FTP site offers a consistent core set of files for the genome sequence and annotation products of all organisms and assembled genomes in scope. It supports download needs including:
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Retrieving the genome sequence for a specific assembled genome
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Retrieving GenBank or RefSeq Gene, RNA, and protein annotation for a specific organism and a specific assembled genome, or a specific RefSeq annotation release
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Retrieving annotation in GenBank flat file, GFF3, or GTF format"><meta property="og:type" content="article"><meta property="og:url" content="/datasets/docs/v2/policies-annotation/genomeftp/"><meta property="article:section" content="policies-annotation"><meta itemprop=name content="NCBI Genomes FTP"><meta itemprop=description content="The Genomes FTP site offers a consistent core set of files for the genome sequence and annotation products of all organisms and assembled genomes in scope. It supports download needs including:
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Retrieving the genome sequence for a specific assembled genome
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Retrieving GenBank or RefSeq Gene, RNA, and protein annotation for a specific organism and a specific assembled genome, or a specific RefSeq annotation release
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Retrieving annotation in GenBank flat file, GFF3, or GTF format"><meta itemprop=wordCount content="1461"><meta itemprop=keywords content><meta name=twitter:card content="summary"><meta name=twitter:title content="NCBI Genomes FTP"><meta name=twitter:description content="The Genomes FTP site offers a consistent core set of files for the genome sequence and annotation products of all organisms and assembled genomes in scope. It supports download needs including:
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Retrieving the genome sequence for a specific assembled genome
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Retrieving GenBank or RefSeq Gene, RNA, and protein annotation for a specific organism and a specific assembled genome, or a specific RefSeq annotation release
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td-sidebar-link__section tree-root" id=m-datasetsdocsv2><span>Documentation</span></a><ul class=ul-1><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2getting_started-li><a href=/datasets/docs/v2/getting_started/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2command-line-toolsdownload-and-install><span>Download and install</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2command-line-toolsusing-dataformat-li><a href=/datasets/docs/v2/command-line-tools/using-dataformat/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2command-line-toolsusing-dataformat><span>Using dataformat</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2command-line-toolsusing-dataformatgene-data-reports-li><a href=/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/ title="Create a table from the gene data reports" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2command-line-toolsusing-dataformatgene-data-reports><span>Gene data reports</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2command-line-toolsusing-dataformatgenome-data-reports-li><a href=/datasets/docs/v2/command-line-tools/using-dataformat/genome-data-reports/ title="Create a table from the genome data reports" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2command-line-toolsusing-dataformatgenome-data-reports><span>Genome data reports</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2command-line-toolsusing-dataformatvirus-data-reports-li><a href=/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/ title="Create a table from the virus data reports" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2command-line-toolsusing-dataformatvirus-data-reports><span>Virus data reports</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2how-tos-li><a href=/datasets/docs/v2/how-tos/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2how-tos><span>How-To Guides</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2how-tosgenes-li><a href=/datasets/docs/v2/how-tos/genes/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2how-tosgenes><span>Genes</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosgenesget-gene-metadata-li><a href=/datasets/docs/v2/how-tos/genes/get-gene-metadata/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2how-tosgenesget-gene-metadata><span>Get gene metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosgenesdownload-gene-data-package-li><a href=/datasets/docs/v2/how-tos/genes/download-gene-data-package/ title="Download a gene data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosgenesdownload-gene-data-package><span>Download genes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosgenesdownload-ortholog-data-package-li><a href=/datasets/docs/v2/how-tos/genes/download-ortholog-data-package/ title="Download an ortholog data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosgenesdownload-ortholog-data-package><span>Download orthologs</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2how-tosgenomes-li><a href=/datasets/docs/v2/how-tos/genomes/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2how-tosgenomes><span>Genomes</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosgenomesget-genome-metadata-li><a href=/datasets/docs/v2/how-tos/genomes/get-genome-metadata/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosgenomesget-genome-metadata><span>Get genome metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosgenomesdownload-genome-li><a href=/datasets/docs/v2/how-tos/genomes/download-genome/ title="Download a genome data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosgenomesdownload-genome><span>Download genome data</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosgenomeslarge-download-li><a href=/datasets/docs/v2/how-tos/genomes/large-download/ title="Download large genome data packages" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosgenomeslarge-download><span>Large genome downloads</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2how-tostaxonomy-li><a href=/datasets/docs/v2/how-tos/taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2how-tostaxonomy><span>Taxonomy</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tostaxonomytaxonomy-li><a href=/datasets/docs/v2/how-tos/taxonomy/taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tostaxonomytaxonomy><span>Get taxonomy metadata</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2how-tosvirus-li><a href=/datasets/docs/v2/how-tos/virus/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2how-tosvirus><span>Virus</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusinfluenza-metadata-li><a href=/datasets/docs/v2/how-tos/virus/influenza-metadata/ title="Get Alphainfluenza virus genome metadata" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusinfluenza-metadata><span>Get Alphainfluenza virus metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusget-influenza-genomes-li><a href=/datasets/docs/v2/how-tos/virus/get-influenza-genomes/ title="Download an Alphainfluenza genome data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusget-influenza-genomes><span>Download Alphainfluenza genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusvirus-metadata-li><a href=/datasets/docs/v2/how-tos/virus/virus-metadata/ title="Get virus genome metadata" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusvirus-metadata><span>Get virus metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusvirus-download-li><a href=/datasets/docs/v2/how-tos/virus/virus-download/ title="Download a virus genome data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusvirus-download><span>Download virus genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusget-sars2-genomes-li><a href=/datasets/docs/v2/how-tos/virus/get-sars2-genomes/ title="Download a SARS-CoV-2 genome data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusget-sars2-genomes><span>Download SARS-CoV-2 genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusget-sars2-proteins-li><a href=/datasets/docs/v2/how-tos/virus/get-sars2-proteins/ title="Download a SARS-CoV-2 protein data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusget-sars2-proteins><span>Download SARS-CoV-2 proteins</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvalidation-li><a href=/datasets/docs/v2/how-tos/validation/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvalidation><span>File validation</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2tutorials-li><a href=/datasets/docs/v2/tutorials/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2tutorials><span>Tutorials</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2tutorialsortholog-get-one-isoform-li><a href=/datasets/docs/v2/tutorials/ortholog-get-one-isoform/ title="Get one protein per gene from a set of orthologs" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2tutorialsortholog-get-one-isoform><span>Get one protein from an ortholog set</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2tutorialsrename-files-li><a href=/datasets/docs/v2/tutorials/rename-files/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2tutorialsrename-files><span>Rename downloaded files</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2tutorialsdownload-ortholog-dataset-li><a href=/datasets/docs/v2/tutorials/download-ortholog-dataset/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2tutorialsdownload-ortholog-dataset><span>Retrieve ortholog data and metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2tutorialsworking-with-jsonl-data-reports-li><a href=/datasets/docs/v2/tutorials/working-with-jsonl-data-reports/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2tutorialsworking-with-jsonl-data-reports><span>Working with JSON Lines data reports</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2api-li><a href=/datasets/docs/v2/api/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2api><span>API</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2apirest-api-li><a href=/datasets/docs/v2/api/rest-api/ title="NCBI Datasets v2 REST API" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2apirest-api><span>REST API</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2apiapi-keys-li><a href=/datasets/docs/v2/api/api-keys/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2apiapi-keys><span>API keys</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2apilanguages-li><a href=/datasets/docs/v2/api/languages/ title="Supported programming languages" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2apilanguages><span>Programming Languages</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2apideprecated-apis-li><a href=/datasets/docs/v2/api/deprecated-apis/ title="Retired API Endpoints" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2apideprecated-apis><span>Retired Endpoints</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child active-path" id=m-datasetsdocsv2policies-annotation-li><a href=/datasets/docs/v2/policies-annotation/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotation><span>NCBI Genome Data Processing</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2policies-annotationgenome-processing-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/ title="NCBI Genome Data Processing" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotationgenome-processing><span>Genome Data Processing</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processingversion-status-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/version-status/ title="Assembly Versioning and Status" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processingversion-status><span>Assembly version and status</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processingreference-selection-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/reference-selection/ title="Selecting Reference Genomes" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processingreference-selection><span>Reference Genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processingrefseq-selection-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/refseq-selection/ title="Genomes Selected for RefSeq Annotation" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processingrefseq-selection><span>RefSeq Genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processinggenome_notes-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/genome_notes/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processinggenome_notes><span>Genome Notes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processingtype-material-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/type-material/ title="What is Type Material?" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processingtype-material><span>Type Material</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2policies-annotationpipelines-li><a href=/datasets/docs/v2/policies-annotation/pipelines/ title="NCBI RefSeq Genome Annotation Pipelines" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotationpipelines><span>Genome Annotation Pipelines</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2policies-annotationquality-li><a href=/datasets/docs/v2/policies-annotation/quality/ title="NCBI Genome Quality Analysis" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotationquality><span>Genome Quality Analysis</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2policies-annotationqualitycontamination-li><a href=/datasets/docs/v2/policies-annotation/quality/contamination/ title="NCBI Contamination Screening" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotationqualitycontamination><span>Contamination Screening</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualitycontaminationfcs-contamination-li><a href=/datasets/docs/v2/policies-annotation/quality/contamination/fcs-contamination/ title="Foreign Contamination Screen (FCS)" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualitycontaminationfcs-contamination><span>FCS</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualitycontaminationani-contamination-li><a href=/datasets/docs/v2/policies-annotation/quality/contamination/ani-contamination/ title="Average Nucleotide Identity (ANI)" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualitycontaminationani-contamination><span>ANI</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualityani-li><a href=/datasets/docs/v2/policies-annotation/quality/ani/ title="Average Nucleotide Identity (ANI)" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualityani><span>ANI Overview</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualitybusco-li><a href=/datasets/docs/v2/policies-annotation/quality/busco/ title="Benchmarking Universal Single-Copy Orthologs (BUSCO) Analysis" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualitybusco><span>BUSCO</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualitycheckm-li><a href=/datasets/docs/v2/policies-annotation/quality/checkm/ title="CheckM Analysis" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualitycheckm><span>CheckM</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2policies-annotationdata-model-li><a href=/datasets/docs/v2/policies-annotation/data-model/ title="The NCBI Genome Assembly Data Model" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationdata-model><span>Data model</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child active-path" id=m-datasetsdocsv2policies-annotationgenomeftp-li><a href=/datasets/docs/v2/policies-annotation/genomeftp/ title="NCBI Genomes FTP" class="align-left ps-0 active td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenomeftp><span class=td-sidebar-nav-active-item>Genomes FTP</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2policies-annotationortholog-calculation-li><a href=/datasets/docs/v2/policies-annotation/ortholog-calculation/ title="How Are Orthologs Calculated?" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationortholog-calculation><span>Ortholog Calculation</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2troubleshooting-li><a href=/datasets/docs/v2/troubleshooting/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2troubleshooting><span>FAQs and troubleshooting</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2troubleshootingfaq-li><a href=/datasets/docs/v2/troubleshooting/faq/ title=FAQs class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2troubleshootingfaq><span>Frequently asked Questions</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2troubleshootingmac-zip-bug-li><a href=/datasets/docs/v2/troubleshooting/mac-zip-bug/ title="Mac zip archive bugs" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2troubleshootingmac-zip-bug><span>Mac zip bugs</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2reference-docs-li><a href=/datasets/docs/v2/reference-docs/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docs><span>Reference</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-line-li><a href=/datasets/docs/v2/reference-docs/command-line/ title="Command line tool reference" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-line><span>Command line</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformat-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedataformat><span>dataformat</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsv-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedataformattsv><span>tsv</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome><span>genome</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome-seq-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_genome-seq/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome-seq><span>genome-seq</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_gene-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_gene><span>gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_gene-product-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_gene-product/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_gene-product><span>gene-product</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_virus-genome-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_virus-genome><span>virus-genome</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_virus-annotation-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-annotation/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_virus-annotation><span>virus-annotation</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_microbigge-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_microbigge/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_microbigge><span>microbigge</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_prok-gene-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_prok-gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_prok-gene><span>prok-gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_prok-gene-location-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_prok-gene-location/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_prok-gene-location><span>prok-gene-location</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome-annotations-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_genome-annotations/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome-annotations><span>genome-annotations</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_taxonomy-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_taxonomy><span>taxonomy</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_organelle-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_organelle/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_organelle><span>organelle</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexcel-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedataformatexcel><span>excel</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome><span>genome</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome-seq-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_genome-seq/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome-seq><span>genome-seq</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_gene-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_gene><span>gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_gene-product-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_gene-product/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_gene-product><span>gene-product</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_virus-genome-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_virus-genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_virus-genome><span>virus-genome</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_virus-annotation-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_virus-annotation/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_virus-annotation><span>virus-annotation</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_microbigge-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_microbigge/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_microbigge><span>microbigge</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_prok-gene-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_prok-gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_prok-gene><span>prok-gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_prok-gene-location-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_prok-gene-location/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_prok-gene-location><span>prok-gene-location</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome-annotations-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_genome-annotations/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome-annotations><span>genome-annotations</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_taxonomy-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_taxonomy><span>taxonomy</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_organelle-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_organelle/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_organelle><span>organelle</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatdataformat_catalog-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/dataformat_catalog/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatdataformat_catalog><span>catalog</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletion-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletion><span>completion</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_bash-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/dataformat_completion_bash/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_bash><span>bash</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_zsh-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/dataformat_completion_zsh/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_zsh><span>zsh</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_fish-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/dataformat_completion_fish/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_fish><span>fish</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_powershell-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/dataformat_completion_powershell/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_powershell><span>powershell</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatdataformat_version-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/dataformat_version/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatdataformat_version><span>version</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasets-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasets><span>datasets</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummary-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetssummary><span>summary</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygene-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygene><span>gene</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_gene-id-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_gene-id/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_gene-id><span>gene-id</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_symbol-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_symbol/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_symbol><span>symbol</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_accession-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_taxon><span>taxon</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_locus-tag-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_locus-tag/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_locus-tag><span>locus-tag</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenome-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenome><span>genome</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_accession-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/genome/datasets_summary_genome_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/genome/datasets_summary_genome_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummaryvirus-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/virus/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetssummaryvirus><span>virus</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummaryvirusgenome-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/virus/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetssummaryvirusgenome><span>genome</span></a><ul class="ul-7 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/virus/genome/datasets_summary_virus_genome_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_taxon><span>taxon</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_accession-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/virus/genome/datasets_summary_virus_genome_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_accession><span>accession</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarytaxonomy-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarytaxonomy><span>taxonomy</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarytaxonomydatasets_summary_taxonomy_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/taxonomy/datasets_summary_taxonomy_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarytaxonomydatasets_summary_taxonomy_taxon><span>taxon</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownload-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownload><span>download</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgene-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgene><span>gene</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_gene-id-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/gene/datasets_download_gene_gene-id/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_gene-id><span>gene-id</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_symbol-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/gene/datasets_download_gene_symbol/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_symbol><span>symbol</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_accession-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/gene/datasets_download_gene_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/gene/datasets_download_gene_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_taxon><span>taxon</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_locus-tag-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/gene/datasets_download_gene_locus-tag/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_locus-tag><span>locus-tag</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenome-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenome><span>genome</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_accession-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/genome/datasets_download_genome_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/genome/datasets_download_genome_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadtaxonomy-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadtaxonomy><span>taxonomy</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadtaxonomydatasets_download_taxonomy_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/taxonomy/datasets_download_taxonomy_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadtaxonomydatasets_download_taxonomy_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirus-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/virus/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirus><span>virus</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusgenome-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/virus/genome/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusgenome><span>genome</span></a><ul class="ul-7 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_accession-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/virus/genome/datasets_download_virus_genome_accession/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/virus/genome/datasets_download_virus_genome_taxon/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusdatasets_download_virus_protein-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/virus/datasets_download_virus_protein/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusdatasets_download_virus_protein><span>protein</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdatasets_rehydrate-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/datasets_rehydrate/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdatasets_rehydrate><span>rehydrate</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletion-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletion><span>completion</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_bash-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/datasets_completion_bash/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_bash><span>bash</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_zsh-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/datasets_completion_zsh/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_zsh><span>zsh</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_fish-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/datasets_completion_fish/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_fish><span>fish</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_powershell-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/datasets_completion_powershell/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_powershell><span>powershell</span></a></li></ul></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docsfile-formats-li><a href=/datasets/docs/v2/reference-docs/file-formats/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsfile-formats><span>File formats</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsannotation-files-li><a href=/datasets/docs/v2/reference-docs/file-formats/annotation-files/ title="Annotation file formats" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsfile-formatsannotation-files><span>Annotation files</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsannotation-filesabout-ncbi-gbff-li><a href=/datasets/docs/v2/reference-docs/file-formats/annotation-files/about-ncbi-gbff/ title="GBFF format" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsannotation-filesabout-ncbi-gbff><span>GBFF</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsannotation-filesabout-ncbi-gff3-li><a href=/datasets/docs/v2/reference-docs/file-formats/annotation-files/about-ncbi-gff3/ title="GFF3 format" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsannotation-filesabout-ncbi-gff3><span>GFF3</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-files-li><a href=/datasets/docs/v2/reference-docs/file-formats/metadata-files/ title="Metadata file formats" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-files><span>Metadata files</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-filesabout-json-and-tabular-li><a href=/datasets/docs/v2/reference-docs/file-formats/metadata-files/about-json-and-tabular/ title="Summary of JSON, JSON Lines, and CSV/TSV tabular formats" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-filesabout-json-and-tabular><span>Summary of metadata file formats</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-fileswhy-jsonl-li><a href=/datasets/docs/v2/reference-docs/file-formats/metadata-files/why-jsonl/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-fileswhy-jsonl><span>Why JSON and JSON Lines</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-filestools-for-jsonl-li><a href=/datasets/docs/v2/reference-docs/file-formats/metadata-files/tools-for-jsonl/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-filestools-for-jsonl><span>Tools for JSON and JSON Lines</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsrelease-notes-li><a href=/datasets/docs/v2/reference-docs/release-notes/ title="NCBI Datasets release notes" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsrelease-notes><span>Release notes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docsdata-reports-li><a href=/datasets/docs/v2/reference-docs/data-reports/ title="Data report schemas" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsdata-reports><span>Report schemas</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportsgene-li><a href=/datasets/docs/v2/reference-docs/data-reports/gene/ title="Gene report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsgene><span>Gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportsgene-product-li><a href=/datasets/docs/v2/reference-docs/data-reports/gene-product/ title="Gene product report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsgene-product><span>Gene product</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportsgenome-assembly-li><a href=/datasets/docs/v2/reference-docs/data-reports/genome-assembly/ title="Genome assembly report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsgenome-assembly><span>Genome assembly</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportsgenome-sequence-li><a href=/datasets/docs/v2/reference-docs/data-reports/genome-sequence/ title="Genome sequence report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsgenome-sequence><span>Genome sequence</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportsmicrobigge-li><a href=/datasets/docs/v2/reference-docs/data-reports/microbigge/ title="MicroBIGG-E report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsmicrobigge><span>MicroBIGG-E</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportsprokaryote-gene-li><a href=/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene/ title="Prokaryote gene report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsprokaryote-gene><span>Prok. gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportsprokaryote-gene-location-li><a href=/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene-location/ title="Prokaryote gene location report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsprokaryote-gene-location><span>Prok. gene location</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportstaxonomy-li><a href=/datasets/docs/v2/reference-docs/data-reports/taxonomy/ title="Taxonomy report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportstaxonomy><span>Taxonomy</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportstaxonomy-names-li><a href=/datasets/docs/v2/reference-docs/data-reports/taxonomy-names/ title="Taxonomy names report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportstaxonomy-names><span>Taxonomy names</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportsvirus-li><a href=/datasets/docs/v2/reference-docs/data-reports/virus/ title="Virus report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsvirus><span>Virus</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-reportsvirus-annotation-li><a href=/datasets/docs/v2/reference-docs/data-reports/virus-annotation/ title="Virus annotation report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsvirus-annotation><span>Virus annotation</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docsdata-packages-li><a href=/datasets/docs/v2/reference-docs/data-packages/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsdata-packages><span>Data packages</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-packagesgene-package-li><a href=/datasets/docs/v2/reference-docs/data-packages/gene-package/ title="NCBI Datasets Gene Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-packagesgene-package><span>Gene package</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-packagesgenome-li><a href=/datasets/docs/v2/reference-docs/data-packages/genome/ title="NCBI Datasets Genome Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-packagesgenome><span>Genome package</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-packagestaxonomy-li><a href=/datasets/docs/v2/reference-docs/data-packages/taxonomy/ title="NCBI Datasets Taxonomy Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-packagestaxonomy><span>Taxonomy package</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-packagesvirus-genome-li><a href=/datasets/docs/v2/reference-docs/data-packages/virus-genome/ title="NCBI Datasets Virus Data Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-packagesvirus-genome><span>Virus data package</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2glossary-li><a href=/datasets/docs/v2/glossary/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2glossary><span>Glossary</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2citing-datasets-li><a href=/datasets/docs/v2/citing-datasets/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2citing-datasets><span>Cite Us</span></a></li></ul></li></ul></nav><script src=/datasets/docs/v2/js/sidebar-tree.js></script><div id=doc-version-selector-container><div>Documentation version</div><select><option value=v2>CLI v16+ (API v2)</option></select>
|
||
<a href=/datasets/docs/v2/troubleshooting/faq/#which-version-of-the-documentation-should-i-use>Learn more</a></div></div></div><div class="d-none d-xl-block col-xl-2 td-sidebar-toc d-print-none"><div class=td-toc><nav id=TableOfContents><ul><li><a href=#faqs>FAQs</a><ul><li><a href=#what-is-the-easiest-way-to-download-data-for-one-or-more-assembled-genomes>What is the easiest way to download data for one or more assembled genomes?</a></li><li><a href=#how-can-i-download-only-the-current-annotation-for-an-organism>How can I download only the current annotation for an organism?</a></li><li><a href=#how-can-i-stay-informed-about-changes-to-the-ncbi-genomes-ftp-site>How can I stay informed about changes to the NCBI genomes FTP site?</a></li><li><a href=#are-files-on-the-ftp-site-updated-following-annotation-updates>Are files on the FTP site updated following annotation updates?</a></li><li><a href=#how-can-i-download-older-annotation-files>How can I download older annotation files?</a></li><li><a href=#what-is-the-file-content-within-each-specific-assembled-genome-directory>What is the file content within each specific assembled genome directory?</a><ul><li><a href=#table-sequence-and-annotation-files-available-on-genomes-ftp>Table: Sequence and Annotation Files Available on Genomes FTP</a></li></ul></li><li><a href=#where-can-i-find-information-to-help-me-choose-between-the-many-different-assembled-genomes-for-a-species>Where can I find information to help me choose between the many different assembled genomes for a species?</a></li><li><a href=#do-you-provide-assembled-genome-data-formatted-for-use-by-sequence-read-alignment-pipelines>Do you provide assembled genome data formatted for use by sequence read alignment pipelines?</a></li><li><a href=#are-repetitive-sequences-in-eukaryotic-genomes-masked>Are repetitive sequences in eukaryotic genomes masked?</a></li></ul></li></ul></nav></div></div><main class="col-12 col-md-9 col-xl-8 pl-md-5" role=main><div id=possible-banner></div><nav aria-label=breadcrumb class=d-print-none><ol class="breadcrumb spb-1"><li class=breadcrumb-item><a href=/datasets/docs/v2/>Documentation</a></li><li class=breadcrumb-item><a href=/datasets/docs/v2/policies-annotation/>NCBI Genome Data Processing</a></li><li class="breadcrumb-item active" aria-current=page><a href=/datasets/docs/v2/policies-annotation/genomeftp/>Genomes FTP</a></li></ol></nav><h1 class="mb-4 font-weight-bold">NCBI Genomes FTP</h1><p class="lead pb-2"></p><div class="d-xl-none td-toc td-toc--inline d-print-none"><a id=td-content__toc-link href=#td-content__toc data-toggle=collapse aria-controls=td-docs-toc aria-expanded=false aria-label="Toggle toc navigation"><span class=lead>Contents<i class="fas fa-chevron-right ml-2"></i></span></a><div id=td-content__toc class=collapse><nav id=TableOfContents><ul><li><a href=#faqs>FAQs</a><ul><li><a href=#what-is-the-easiest-way-to-download-data-for-one-or-more-assembled-genomes>What is the easiest way to download data for one or more assembled genomes?</a></li><li><a href=#how-can-i-download-only-the-current-annotation-for-an-organism>How can I download only the current annotation for an organism?</a></li><li><a href=#how-can-i-stay-informed-about-changes-to-the-ncbi-genomes-ftp-site>How can I stay informed about changes to the NCBI genomes FTP site?</a></li><li><a href=#are-files-on-the-ftp-site-updated-following-annotation-updates>Are files on the FTP site updated following annotation updates?</a></li><li><a href=#how-can-i-download-older-annotation-files>How can I download older annotation files?</a></li><li><a href=#what-is-the-file-content-within-each-specific-assembled-genome-directory>What is the file content within each specific assembled genome directory?</a><ul><li><a href=#table-sequence-and-annotation-files-available-on-genomes-ftp>Table: Sequence and Annotation Files Available on Genomes FTP</a></li></ul></li><li><a href=#where-can-i-find-information-to-help-me-choose-between-the-many-different-assembled-genomes-for-a-species>Where can I find information to help me choose between the many different assembled genomes for a species?</a></li><li><a href=#do-you-provide-assembled-genome-data-formatted-for-use-by-sequence-read-alignment-pipelines>Do you provide assembled genome data formatted for use by sequence read alignment pipelines?</a></li><li><a href=#are-repetitive-sequences-in-eukaryotic-genomes-masked>Are repetitive sequences in eukaryotic genomes masked?</a></li></ul></li></ul></nav></div><button id=td-content__toc-link-expanded href=#td-content__toc class="btn btn-small ml-1 my-2 py-0 px-3" data-toggle=collapse aria-controls=td-docs-toc aria-expanded=true aria-label="Toggle toc navigation"></button></div><style>.td-content table{border:1px solid #ccc}@media screen and (min-width:600px){.td-content table{display:table}}@media screen and (max-width:400px){.td-content table td{white-space:nowrap!important}}.td-content table th{white-space:nowrap}summary>h3{display:inline-block}</style><div class=td-content><h1>NCBI Genomes FTP</h1><header class=article-meta></header><p>The Genomes FTP site offers a consistent core set of files for the genome sequence and annotation products of all organisms and assembled genomes in scope. It supports download needs including:</p><ul><li><p>Retrieving the genome sequence for a specific assembled genome</p></li><li><p>Retrieving GenBank or RefSeq Gene, RNA, and protein annotation for a specific organism and a specific assembled genome, or a specific RefSeq annotation release</p></li><li><p>Retrieving annotation in GenBank flat file, GFF3, or GTF format</p></li><li><p>Retrieving RefSeq annotation for <a href=https://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/>mitochondria</a>, <a href=https://ftp.ncbi.nlm.nih.gov/refseq/release/plastid/>plastids</a>, and <a href=https://ftp.ncbi.nih.gov/genomes/refseq/plasmid/>plasmids</a></p></li><li><p>Assembly summary reports containing metadata for the latest and historical GenBank and RefSeq assembled genomes</p></li><li><p>Matching set of sequence (FASTA) and annotation (GFF3 or GTF) files with identical sequence identifiers to facilitate reproducible analyses</p></li><li><p>MD5 checksums to ensure downloaded content is complete</p></li></ul><h2 id=faqs>FAQs</h2><h3 id=what-is-the-easiest-way-to-download-data-for-one-or-more-assembled-genomes>What is the easiest way to download data for one or more assembled genomes?</h3><ul><li>Using <a href=https://www.ncbi.nlm.nih.gov/datasets/>NCBI Datasets</a>. This is the most user-friendly way to download genome data. Please see NCBI Datasets <a href=https://www.ncbi.nlm.nih.gov/datasets/docs/v2/>Documentation</a> for more details.</li><li>From the <a href=https://ftp.ncbi.nlm.nih.gov/genomes>Genomes FTP</a> site: Users interested in additional files that are currently not included in the Datasets package (see table) can browse the Genomes FTP site to download them piecemeal or download in bulk using command-line tools such as lftp and rsync.</li></ul><h3 id=how-can-i-download-only-the-current-annotation-for-an-organism>How can I download only the current annotation for an organism?</h3>Most users will want to download data only for the latest annotation for the reference assembled genome of an organism. This data is available in <a href=https://www.ncbi.nlm.nih.gov/datasets/>NCBI Datasets</a>.<h3 id=how-can-i-stay-informed-about-changes-to-the-ncbi-genomes-ftp-site>How can I stay informed about changes to the NCBI genomes FTP site?</h3>Subscribe to the <a href=https://ncbi.nlm.nih.gov/mailman/listinfo/genomes-announce>Genomes-announce</a> mailing list or follow the <a href=https://ncbiinsights.ncbi.nlm.nih.gov/>NCBI Insights</a> blog.<h3 id=are-files-on-the-ftp-site-updated-following-annotation-updates>Are files on the FTP site updated following annotation updates?</h3>All new annotation releases are published to the <a href=https://ftp.ncbi.nlm.nih.gov/genomes>Genomes FTP</a> site.<h3 id=how-can-i-download-older-annotation-files>How can I download older annotation files?</h3>NCBI Datasets delivers the latest annotation for any assembled genome version. In some cases, when an assembled genome is annotated multiple times by NCBI and users need data for a specific older annotation release for that assembled genome, they can download it from the <a href=https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases>annotation_releases</a> directory on the <a href=https://ftp.ncbi.nlm.nih.gov/genomes>Genomes FTP</a> site.<h3 id=what-is-the-file-content-within-each-specific-assembled-genome-directory>What is the file content within each specific assembled genome directory?</h3>Directories for all current assembled genomes, and for many previous versions, include a core set of files, plus additional files relevant to the specific assembled genome. Directories for old, assembled genome versions that predate the genomes FTP site reorganization contain only the assembly report, assembly stats, and assembly status files (see table).<h4 id=table-sequence-and-annotation-files-available-on-genomes-ftp>Table: Sequence and Annotation Files Available on Genomes FTP</h4><table><thead><tr><th style=text-align:left>File</th><th style=text-align:left>Format</th><th style=text-align:left>Description</th></tr></thead><tbody><tr><td style=text-align:left>*_ani_contam_ranges.tsv [G/R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports potentially contaminated regions in the assembly identified based on <a href=/datasets/docs/v2/policies-annotation/quality/contamination/ani-contamination/>Average Nucleotide Identity (ANI).</a></td></tr><tr><td style=text-align:left>*_ani_report.txt [G/R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports <a href=/datasets/docs/v2/policies-annotation/quality/contamination/ani-contamination/>Average Nucleotide Identity (ANI)</a>
|
||
based evaluation of the taxonomic identity of the assembly.</td></tr><tr><td style=text-align:left>*_assembly_regions.txt [R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports the location of genomic regions and lists the alt/patch scaffolds placed within those regions.</td></tr><tr><td style=text-align:left>*_assembly_report.txt [G/R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports the name, role, and sequence accession.version for objects in the assembly.</td></tr><tr><td style=text-align:left>*_assembly_stats.txt [G/R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports statistics for the assembly.</td></tr><tr><td style=text-align:left>*_cds_from_genomic.fna.gz [D/G/R]</td><td style=text-align:left>FASTA</td><td style=text-align:left>Nucleotide sequences corresponding to all CDS features annotated on the assembly, based on the genome sequence.</td></tr><tr><td style=text-align:left>*_fcs_report.txt [G/R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports potentially contaminated regions in the assembly identified by the <a href=/datasets/docs/v2/policies-annotation/quality/contamination/fcs-contamination/>Foreign Contamination Screen (FCS).</a></td></tr><tr><td style=text-align:left>*_feature_count.txt.gz [G/R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports counts of gene, RNA, CDS, and similar features based on data reported in the *_feature_table.txt.gz file.</td></tr><tr><td style=text-align:left>*_feature_table.txt.gz [G/R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports locations and attributes for a subset of annotated features.</td></tr><tr><td style=text-align:left>*_gene_expression_counts.txt.gz [R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports counts of RNA-seq reads mapped to each gene.</td></tr><tr><td style=text-align:left>*_normalized_gene_expression_counts.txt.gz [R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports normalized counts (TPM) of RNA-seq reads mapped to each gene.</td></tr><tr><td style=text-align:left>*_gene_ontology.gaf.gz [R]</td><td style=text-align:left>GO Annotation File (GAF)</td><td style=text-align:left>Gene Ontology (GO) annotation of the annotated genes.</td></tr><tr><td style=text-align:left>*_genomic.fna.gz [D/G/R]</td><td style=text-align:left>FASTA</td><td style=text-align:left>Genomic sequence(s) in the assembly. Repetitive sequences in eukaryotes are masked to lower-case.</td></tr><tr><td style=text-align:left>*_genomic.gbff.gz [G/R]</td><td style=text-align:left>GenBank flat file</td><td style=text-align:left>Genomic sequence(s) in the assembly.</td></tr><tr><td style=text-align:left>*_genomic.gff.gz [D/G/R]</td><td style=text-align:left>GFF3</td><td style=text-align:left>Annotation of the genomic sequence(s).</td></tr><tr><td style=text-align:left>*_genomic.gtf.gz [D/G/R]</td><td style=text-align:left>GTF</td><td style=text-align:left>Annotation of the genomic sequence(s).</td></tr><tr><td style=text-align:left>*_genomic_gaps.txt.gz [G/R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports the coordinates of all gaps in the top-level genomic sequences.</td></tr><tr><td style=text-align:left>*_protein.faa.gz [D/G/R]</td><td style=text-align:left>FASTA</td><td style=text-align:left>Sequences of accessioned protein products annotated on the genome assembly.</td></tr><tr><td style=text-align:left>*_protein.gpff.gz [G/R]</td><td style=text-align:left>GenPept flat file</td><td style=text-align:left>Sequences of accessioned protein products annotated on the genome assembly.</td></tr><tr><td style=text-align:left>*_pseudo_without_product.fna.gz [R]</td><td style=text-align:left>FASTA</td><td style=text-align:left>Genomic sequence corresponding to pseudogene and other gene regions which do not have any associated transcribed RNA products or translated protein products.</td></tr><tr><td style=text-align:left>*_rm.out.gz [R]</td><td style=text-align:left>Text</td><td style=text-align:left>RepeatMasker output (provided for some eukaryotes).</td></tr><tr><td style=text-align:left>*_rm.run [R]</td><td style=text-align:left>Text</td><td style=text-align:left>Documentation of the RepeatMasker version, parameters, and library (provided for some eukaryotes).</td></tr><tr><td style=text-align:left>*_rna.fna.gz [D/R]</td><td style=text-align:left>FASTA</td><td style=text-align:left>Sequences of accessioned RNA products annotated on the genome assembly.</td></tr><tr><td style=text-align:left>*_rna.gbff.gz [R]</td><td style=text-align:left>GenBank flat file</td><td style=text-align:left>RNA products annotated on the genome assembly (provided for RefSeq assemblies as relevant).</td></tr><tr><td style=text-align:left>*_rna_from_genomic.fna.gz [G/R]</td><td style=text-align:left>FASTA</td><td style=text-align:left>Nucleotide sequences corresponding to all RNA features annotated on the assembly, based on the genome sequence.</td></tr><tr><td style=text-align:left>*_rnaseq_alignment_summary.txt [R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports counts of alignments classified by Subread featureCounts.</td></tr><tr><td style=text-align:left>*_rnaseq_runs.txt [R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Information about RNA-seq runs used for gene expression analyses.</td></tr><tr><td style=text-align:left>*_translated_cds.faa.gz [G/R]</td><td style=text-align:left>FASTA</td><td style=text-align:left>Individual CDS features annotated on the genomic records, conceptually translated into protein sequences.</td></tr><tr><td style=text-align:left>*_wgsmaster.gbff.gz [G]</td><td style=text-align:left>GenBank flat file</td><td style=text-align:left>WGS master for the assembly (present only if a WGS master record exists for the sequences in the assembly)</td></tr><tr><td style=text-align:left>.annotation_hashes.txt [G/R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Reports hash values for different aspects of the annotation data</td></tr><tr><td style=text-align:left>.assembly_status.txt [G/R]</td><td style=text-align:left>Text</td><td style=text-align:left>Reports the current status of this assembly version</td></tr><tr><td style=text-align:left>.md5checksums.txt [G/R]</td><td style=text-align:left>Text</td><td style=text-align:left>File checksums are provided for all data files in the directory.</td></tr><tr><td style=text-align:left>*_knownrefseq_alns.bam (RefSeq_transcripts_alignments sub-directory) [R]</td><td style=text-align:left>BAM</td><td style=text-align:left>Alignments of the annotated Known RefSeq transcripts (identified with accessions prefixed with NM_ and NR_) to the genome.</td></tr><tr><td style=text-align:left>*_knownrefseq_alns.bam.bai (RefSeq_transcripts_alignments sub-directory) [R]</td><td style=text-align:left>BAM Index</td><td style=text-align:left>Index of the BAM alignments of the annotated Known RefSeq transcripts to the genome.</td></tr><tr><td style=text-align:left>*_modelrefseq_alns.bam (RefSeq_transcripts_alignments sub-directory) [R]</td><td style=text-align:left>BAM</td><td style=text-align:left>Alignments of the annotated Model RefSeq transcripts (identified by accessions prefixed with XM_ and XR_) to the genome.</td></tr><tr><td style=text-align:left>*_modelrefseq_alns.bam.bai (RefSeq_transcripts_alignments sub-directory) [R]</td><td style=text-align:left>BAM Index</td><td style=text-align:left>Index of the BAM alignments of the annotated Model RefSeq transcripts to the genome.</td></tr><tr><td style=text-align:left>*_compare_prev.txt.gz (Annotation_comparison sub-directory) [R]</td><td style=text-align:left>Tab-delimited text</td><td style=text-align:left>Annotation comparison report.</td></tr><tr><td style=text-align:left>*_cross_species_tx_alns.gff.gz (Evidence_alignments sub-directory) [R]</td><td style=text-align:left>GFF3</td><td style=text-align:left>Alignments of cDNAs, ESTs, and TSAs from other species to the genomic sequence(s).</td></tr><tr><td style=text-align:left>*_same_species_tx_alns.gff.gz (Evidence_alignments sub-directory) [R]</td><td style=text-align:left>GFF3</td><td style=text-align:left>Alignments of same species cDNAs, ESTs, and TSAs to the genomic sequence(s).</td></tr><tr><td style=text-align:left>*_gnomon_model.gff.gz (Gnomon_models sub-directory) [R]</td><td style=text-align:left>GFF3</td><td style=text-align:left>Gnomon annotation of the genomic sequence(s).</td></tr><tr><td style=text-align:left>*_gnomon_protein.faa.gz (Gnomon_models sub-directory) [R]</td><td style=text-align:left>FASTA</td><td style=text-align:left>Gnomon protein models annotated on the genome assembly.</td></tr><tr><td style=text-align:left>*_gnomon_rna.fna.gz (Gnomon_models sub-directory) [R]</td><td style=text-align:left>FASTA</td><td style=text-align:left>Gnomon transcript models annotated on the genome assembly.</td></tr><tr><td style=text-align:left>*_graph.bw (RNASeq_coverage_graphs directory) [R]</td><td style=text-align:left>UCSC BigWig</td><td style=text-align:left>RNA-seq read coverage graphs. Alternative style: subdir/*_file.txt</td></tr></tbody></table><p><em>D: Datasets; G: Genbank; R: RefSeq</em></p><p>* Sample file path with either a GCA or GCF prefix where each hashtag represents a number in the actual path: <code>https://ftp.ncbi.nih.gov/genomes/all/GC[A/F]/###/###/###/GC[A/F]_#########_(assembly name)/GC[A/F]_#########_(assembly name)</code></p><h3 id=where-can-i-find-information-to-help-me-choose-between-the-many-different-assembled-genomes-for-a-species>Where can I find information to help me choose between the many different assembled genomes for a species?</h3><p>Many different assembled genomes are available for species with medical, agricultural, or scientific relevance. The Genus_species directories under the “genbank” and “refseq” directory trees each contain an <code>assembly_summary.txt</code> file that provides general information on all assembled genome versions included in the directory such as release date, submitter organization, assembly level, and annotation status. For example, see <a href=https://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/Apis_mellifera/assembly_summary.txt>https://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/Apis_mellifera/assembly_summary.txt</a>.</p><p>After assembled genomes of interest have been identified using the data from the species-specific assembly_summary.txt file, they can be accessed via the “all_assembly_versions” directory for that species. Alternatively, any assembled genomes the <a href=https://ncbi.nlm.nih.gov/refseq>NCBI Reference Sequence Database (RefSeq)</a> selects as reference genome can be readily accessed via the directory named “reference” in the Genus_species directories under the “genbank” and “refseq” directory trees.</p><h3 id=do-you-provide-assembled-genome-data-formatted-for-use-by-sequence-read-alignment-pipelines>Do you provide assembled genome data formatted for use by sequence read alignment pipelines?</h3><p>Genomic FASTA with modified sequence identifiers and index files
|
||
convenient for analysis with Next Generation Sequencing tools are
|
||
currently provided for the Genome Reference Consortium’s human and mouse
|
||
assembled genomes <a href=https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids>GRCh38</a>, <a href=https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.5_GRCm38.p3/seqs_for_alignment_pipelines.ucsc_ids>GRCm38.p3</a>,
|
||
and <a href=https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.9_GRCm39/seqs_for_alignment_pipelines.ucsc_ids>GRCm39</a>.
|
||
RefSeq annotation in GFF3 and GTF formats with sequence identifiers matching those in the FASTA files are also provided to facilitate use in RNA-Seq analysis pipelines.</p><p>The four analysis sets provided for GRCh38 (no_alt_analysis_set, full_analysis_set, full_plus_hs38d1_analysis_set, and no_alt_plus_hs38d1_analysis_set) and the two analysis sets provided for GRCm38.p3 (no_alt_analysis_set and full_analysis_set) differ from the corresponding full assembled genomes by one or more of the following:</p><ul><li>omission of alternate locus and patch scaffolds that cause complications for sequence read alignment programs that are not alternate contig aware (alt-aware)</li><li>hard masking of duplicate copies of pseudo-autosomal regions and centromeric arrays</li><li>addition of “decoy” sequences</li></ul><p>Additionally, index files generated by BWA, Samtools, Bowtie, and HISAT2
|
||
are also provided. See the <a href=https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/README_analysis_sets.txt>GRCh38 README</a>, <a href=https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.5_GRCm38.p3/seqs_for_alignment_pipelines.ucsc_ids/README_analysis_sets.txt>GRCm38 README</a>, or <a href=https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.9_GRCm39/seqs_for_alignment_pipelines.ucsc_ids/README_analysis_sets.txt>GRCm39 README</a> for a full description.</p><h3 id=are-repetitive-sequences-in-eukaryotic-genomes-masked>Are repetitive sequences in eukaryotic genomes masked?</h3><p>Yes. All genome sequences are softmasked using <a href=https://doi.org/10.1093/bioinformatics/bti774>WindowMasker</a> or <a href=https://www.repeatmasker.org/>RepeatMasker</a>.
|
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For genomes that are masked using RepeatMasker, an additional file with information about the masked regions is also provided (see table above).</p>Generated March 11, 2025</div><div class=c-global-meta-links><div class="td-page-meta ml-2 pb-1 pt-2 mb-0"></div></div></main></div></div></div><footer><section class=icon-section><div id=icon-section-header class=icon-section_header>Follow NCBI</div><div class="grid-container container"><div class=icon-section_container><a class=footer-icon id=footer_twitter href=https://twitter.com/ncbi aria-label=Twitter><svg width="40" height="40" viewBox="0 0 40 37" fill="none" xmlns="http://www.w3.org/2000/svg"><title>Twitter</title><g id="twitterx1008"><path id="path1008" d="M6.06736 7 16.8778 20.8991 6.00001 32.2H10.2l8.4-9.1 7.068 9.1H34L22.8 17.5 31.9 7H28.4l-7.7 8.4L14.401 7H6.06898 6.06736zM9.66753 8.73423H12.9327l16.8 21.73157h-3.163L9.66753 8.73423z" fill="#5b616b"/></g></svg></a><a class=footer-icon id=footer_facebook 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