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<h1 id="amrfinderplus">AMRFinderPlus</h1>
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<p>NCBI has developed AMRFinderPlus, a tool that identifies AMR genes, resistance-associated point mutations, and select other classes of genes using protein annotations and/or assembled nucleotide sequence. AMRFinderPlus is used in the <a href="/pathogens/pathogens_help/#data-processing">Pathogen Detection pipeline</a>, and these data are displayed in <a href="/pathogens/isolates/">NCBI’s Isolate Browser</a>. AMRFinderPlus relies on NCBI’s curated <a href="/pathogens/isolates#/refgene/">Reference Gene Database</a> and curated collection of <a href="https://ftp.ncbi.nlm.nih.gov/hmm/NCBIfam-AMRFinder/latest">Hidden Markov Models</a>. For more information on how AMRFinderPlus operates, please see the <a href="https://github.com/ncbi/amr/wiki/Methods">Methods section</a> of the <a href="https://github.com/ncbi/amr/wiki">AMRFinderPlus documentation</a>. See our <a href="/pathogens/pathogens_help/#amr">documentation</a> for a description of all our <a href="../">NCBI antimicrobial resistance resources</a>.</p>
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<h3 id="ncbi-has-made-amrfinderplus-soft">NCBI has made AMRFinderPlus software and databases open source and freely available</h3>
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<ul>
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<li><a href="https://github.com/ncbi/amr/wiki">Documentation</a></li>
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<li><a href="https://github.com/ncbi/amr/wiki/Installing-AMRFinder">Installation instructions</a></li>
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<li><a href="https://github.com/ncbi/amr/releases">Software releases</a></li>
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<li><a href="https://github.com/ncbi/amr">Source code</a></li>
|
||
<li><a href="/pathogens/isolates#/refgene/">Pathogen Detecton Reference Gene Catalog</a> Includes web interface for AMR genes, point mutations, and other classes of genes</li>
|
||
<li><a href="/pathogens/hmm/">Pathogen Detecton Reference HMM Catalog</a> Includes web interface for carefully curated HMMs used by AMRFinderPlus to identify AMR genes, and some stress and virulence proteins</li>
|
||
<li><a href="/bioproject/PRJNA313047">Bacterial Antimicrobial Resistance Reference Gene Database</a> Bioproject containing curated AMR gene reference sequences only</li>
|
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<li><a href="https://ftp.ncbi.nlm.nih.gov/hmm/NCBIfam-AMRFinder/latest">NCBIfam-AMRFinder</a> Curated AMRFinderPlus HMM library</li>
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</ul>
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<h3 id="ncbi-runs-amrfinderplus-on-hundr">NCBI runs AMRFinderPlus on hundreds of thousands of isolates as part of the Pathogen Detection pipeline and makes the results publically available</h3>
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<ul>
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<li><a href="/pathogens/isolates#/search/">Pathogen Detection Isolates Browser</a> Includes genes found by AMRFinderPlus in the
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<a href="/pathogens/pathogens_help/#data-field-AMRGenotypes">AMR genotypes</a>,
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||
<a href="/pathogens/pathogens_help/#data-field-stress-genotypes">Stress genotypes</a>, and
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||
<a href="/pathogens/pathogens_help/#data-field-virulence-genotypes">Virulence genotypes</a> columns</li>
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<li><a href="/pathogens/pathogens_help/#isolates-browser">Pathogen Detection Isolates Browser documentation</a></li>
|
||
<li><a href="/pathogens/microbigge/">MicroBIGG-E</a> (<strong>Micro</strong>bial <strong>B</strong>rowser for <strong>I</strong>dentification of <strong>G</strong>enetic and <strong>G</strong>enomic <strong>E</strong>lements) contains detailed AMRFinderPlus results and associated metadata for individual AMRFinderPlus hits. Note that there may be a delay between when isolates appear in the isolates browser and when MicroBIGG-E results appear because MicroBIGG-E results are only available for isolates that have public assembly accessions.</li>
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<li><a href="/pathogens/pathogens_help/#microbigge">MicroBIGG-E documentation</a></li>
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</ul>
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<h3 id="a-note-about-abricate">A note about ABRicate</h3>
|
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|
||
<p>Many people are using <a href="https://github.com/tseemann/abricate">ABRicate</a> with the
|
||
default "ncbi" database, and it has come to our attention that at least some
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users are confused that they are getting the same or similar results to what
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||
they would get from AMRFinderPlus. ABRicate uses a subset of the AMRFinderPlus
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database to do AMR gene detection and different methods so the results are not
|
||
the same as those you get by running AMRFinderPlus. To identify AMR genes from
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assembled sequence we recommend using
|
||
<a href="https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus">AMRFinderPlus</a> to get
|
||
the full value out of the NCBI compiled database, including correct allele and
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gene symbols, named allele vs. novel allele determination, protein-based
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search/naming, curated cutoffs, HMM searches, etc.</p>
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<hr/>
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<p>If you have questions about the database or software, or experience problems with AMRFinderPlus please contact <a href="mailto:pd-help@ncbi.nlm.nih.gov">pd-help@ncbi.nlm.nih.gov</a></p>
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<p><a href="http://www.ncbi.nlm.nih.gov/mailman/listinfo/amrfinder-announce">Subscribe to the amrfinder-announce mailing list</a> to get updates when we release new versions of the software or database. This is a low-traffic list.</p>
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