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<h1 id="agp-validation">AGP Validation</h1>
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<p>AGP file structure and content can be validated using the agp_validate program. The on-line version of agp_validate checks that the input AGP file conforms to the <a href="/genbank/genome_agp_specification/">AGP format Specification</a>, checks the file for internal consistency, and generates a report of component, gap, scaffold and object statistics. The command-line version of agp_validate performs all the same checks as the on-line version but also has options to perform additional checks by comparing the AGP to sequences in FASTA files (see below).</p>
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<h2 id="agp-validation-online">AGP validation on-line</h2>
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<p>The on-line <a href="/projects/genome/assembly/agp/agp_validate.cgi">AGP Validation form</a> can be used to run agp_validate on an uploaded AGP file or on AGP text pasted into the form.</p>
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<h2 id="agp_validate-commandline-program">agp_validate command-line program</h2>
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<p>agp_validate is available by anonymous <a href="https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/agp_validate/">FTP</a>. Copy the appropriate version for your platform, then uncompress the file, rename it to "agp_validate", and set the "execute" permission (see <a href="https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/agp_validate/README">platform-specific details</a>).</p>
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<p><span class="tag">usage overview:</span> agp_validate [-options] [FASTA files...] [AGP files...]</p>
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<ul>
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<li>Run without any options agp_validate will perform a large number of validations on the input AGP files (see below), and will also generate a report of component, gap, scaffold and object statistics.</li>
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<li>If component FASTA sequence files are provided, agp_validate will also check that component spans do not exceed the sequence length.</li>
|
|
<li>If the component sequences are available in GenBank, then agp_validate can perform additional checks using the sequence lengths, versions, and taxonomy ID retrieved from GenBank (-alt and -species options).</li>
|
|
<li>If FASTA sequences for the assembled objects are provided, agp_validate can also check that the sequences match what can be constructed from the AGP and the component sequences (-comp option).</li>
|
|
<li>Information on all the available options can be obtained by executing agp_validate with the -help option.</li>
|
|
</ul>
|
|
|
|
|
|
<h2 id="validations-performed-by-agp_val">Validations performed by agp_validate</h2>
|
|
|
|
|
|
<h3 id="error-level-violations-reported-">Error level violations reported include:</h3>
|
|
|
|
|
|
<ul>
|
|
<li>Incorrect number of columns: there should be 9 tab-separated columns.</li>
|
|
<li>Non-positive integers in the following columns:<ul>
|
|
<li>2: object_beg</li>
|
|
<li>3: object_end</li>
|
|
<li>4: part_number</li>
|
|
<li>6b: gap_length</li>
|
|
<li>7a: component_beg</li>
|
|
<li>8a: component_end</li>
|
|
</ul>
|
|
</li>
|
|
<li>object_end is less than the object_beg.</li>
|
|
<li>component_end is less than the component_beg.</li>
|
|
<li>The length of the span specified for the component (in column 7a and 8a) does not match the length of the span specified for the object (in column 2 and 3).</li>
|
|
<li>The length specified for the gap (in column 6b) does not match the length of the span specified for the object (in column 2 and 3).</li>
|
|
<li>Linkage=yes with a gap_type other than scaffold or repeat.</li>
|
|
<li>Object does not start with an object_beg coordinate of 1.</li>
|
|
<li>Object has ranges that are non-sequential and/or overlapping.</li>
|
|
<li>Object does not start with a part_number of 1.</li>
|
|
<li>Object has non-sequential lines and/or lines mixed with other objects.</li>
|
|
<li>Multiple objects with the same object name (column 1).</li>
|
|
<li>Component orientation of 0 or na used for a non-singleton scaffold.</li>
|
|
<li>Invalid terms or symbols in the following columns:<ul>
|
|
<li>5: component_type</li>
|
|
<li>7b: gap_type</li>
|
|
<li>8b: linkage</li>
|
|
<li>9a: orientation</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
|
|
<h3 id="warning-level-violations-reporte">Warning level violations reported include:</h3>
|
|
|
|
|
|
<ul>
|
|
<li>Gap at the beginning or the end of an object.</li>
|
|
<li>Consecutive gap lines of the same type.</li>
|
|
<li>Overlapping spans used for a given component_id.</li>
|
|
<li>Non-draft component_id used more than once.</li>
|
|
<li>Non-draft component spans out of order.</li>
|
|
<li>Extra tab character at the end of the line.</li>
|
|
<li>Component type is not consistent with the line format.</li>
|
|
<li>Component type is not consistent with the component_id accession.</li>
|
|
</ul>
|
|
|
|
|
|
<h3 id="additional-errors-and-warnings-r">Additional errors and warnings reported when optional validations are invoked:</h3>
|
|
|
|
|
|
<ul>
|
|
<li>Invalid component_id. [-alt or -g option]</li>
|
|
<li>Component is not in GenBank. [-alt option]</li>
|
|
<li>component_id is ambiguous without an explicit version. [-alt option]</li>
|
|
<li>component_end is greater than the sequence length. [-alt option, or FASTA files provided]</li>
|
|
</ul>
|
|
|
|
|
|
<p><span id="shared-content-1"></span></p>
|
|
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|
|
</div>
|
|
<!--/.col1-->
|
|
<div class="col2">
|
|
<div class="rightnav">
|
|
<h2 id="genome-resources">Genome Resources</h2>
|
|
<ul>
|
|
<li><a href="/genbank/wgs/">About WGS</a></li>
|
|
<li><a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/?view=wgs">WGS Browser</a></li>
|
|
<li><a href="/genbank/genomesubmit/">Genome Submission Guide</a></li>
|
|
<li><a href="https://submit.ncbi.nlm.nih.gov/subs/genome/">Genome Submission Portal</a></li>
|
|
<li><a href="/genbank/wgs_update/">Update Genome Records</a></li>
|
|
<li><a href="/genbank/wgsfaq/">FAQ</a></li>
|
|
<li><a href="/genbank/table2asn">table2asn</a></li>
|
|
<li><a href="/genbank/diploid_haps">Submitting Multiple Haplotype Assemblies</a></li>
|
|
<li><a href="/WebSub/template.cgi/">Create Submission Template</a></li>
|
|
<li><a href="/genbank/eukaryotic_genome_submission/">Eukaryotic Annotation Guide</a></li>
|
|
<li><a href="/genbank/genomesubmit_annotation/">Prokaryotic Annotation Guide</a></li>
|
|
<li><a href="/genbank/examples.wgs/">Annotation Example Files</a></li>
|
|
<li><a href="/genbank/genomes_gff">Annotating Genomes with GFF3 or GTF files</a></li>
|
|
<li><a href="/genbank/genome_validation">Validation Error Explanations for Genomes</a></li>
|
|
<li><a href="/genbank/asndisc/">Discrepancy Report</a></li>
|
|
<li><a href="https://www.ncbi.nlm.nih.gov/genome/annotation_prok/">NCBI Prokaryotic Genome Annotation Pipeline</a></li>
|
|
<li><a href="https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/">AGP Format</a></li>
|
|
<li><a href="/genbank/metagenome/">Metagenome Submission Guide</a></li>
|
|
<li><a href="/genbank/structuredcomment/">Structured Comment</a></li>
|
|
<li><a href="/bioproject/">BioProject</a></li>
|
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<li><a href="/biosample/">BioSample</a></li>
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</ul>
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