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Metagenome Assembly
<!DOCTYPE html> <html lang="en"> <head> <meta charset="UTF-8" /> <meta property="og:title" content="Metagenome Assembly" /> <meta property="og:url" content="https://www.ddbj.nig.ac.jp/ddbj/metagenome-assembly-e.html" /> <meta property="og:description" content="Microorganisms comprise the majority of the planet’s biologicaldiversity, howeve..." /> <meta property6="og:image" content="/images/thumbnail/logo_ddbj_fb.png" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <title>Metagenome Assembly</title> <script async src="https://www.google-analytics.com/analytics.js"></script> <script src="https://code.jquery.com/jquery-3.5.0.js" integrity="sha256-r/AaFHrszJtwpe+tHyNi/XCfMxYpbsRg2Uqn0x3s2zc=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery.hoverintent/1.10.1/jquery.hoverIntent.min.js" integrity="sha512-gx3WTM6qxahpOC/hBNUvkdZARQ2ObXSp/m+jmsEN8ZNJPymj8/Jamf8+/3kJQY1RZA2DR+KQfT+b3JEB0r9YRg==" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/spin.js/4.1.0/spin.min.js" integrity="sha512-CbohqWjAgarTqRHcX1MbwkF2pujwbsCee1PABpnBWC+VqSldvlNEEI5+4OSsR/HbFQOFFpwY2YvZZNjBMxNnXg==" crossorigin="anonymous"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery.colorbox/1.6.4/jquery.colorbox-min.js"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery-deparam/0.5.3/jquery-deparam.min.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.trace.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.json_search.js"></script> <link rel="icon" href="https://www.ddbj.nig.ac.jp/assets/images/favicon_ddbj.ico"> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/colorbox.css" /> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/main.css" /> <link rel="alternate" type="application/rss+xml" title="My Site RSS" href="/feed.xml" /> <script src="https://www.ddbj.nig.ac.jp/assets/js/main.js"></script> </head> <body data-category="ddbj"> <script src="https://www.ddbj.nig.ac.jp/assets/js/ddbj_common_framework.js" id="DDBJ_common_framework" style="display: block; 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By standard genome analysis methods requiring isolation and laboratory cultivation, limited knowledge was gained regarding these uncultured microorganisms. Metagenomics is a culture-independent genomic analysis method which surveys genomes of uncultured microorganisms and has brought new discoveries about the genetic diversity, population structure and ecological roles of these uncultured microorganisms.</p> <p>Data from metagenome projects are grouped into four groups depending on their assembly level.</p> <p>(1) NGS raw reads before assembly. (2) Assembled contigs of unknown taxa (Primary metagenome). (3) Binned assemblies asserted to known taxonomies (Binned metagenome). (4) A highest quality (in terms of completeness and contamination) representative binned assembly (Metagenome-Assembled Genome, MAG) for each predicted species.</p> <p>DDBJ Center accepts (1)-(3) in DRA and (4) in DDBJ. Regarding quality of MAG assembly, please refer to <a href="https://www.nature.com/articles/nbt.3893">this publication</a>.</p> <p>This guide explains how to submit these metagenomic sequencing data to the BioProject/BioSample/DRA/DDBJ. Raw sequencing data deposition to DRA is basically required.</p> <h2 id="mag-submission">Submission of metagenome assembly data</h2> <div class="figure"> <a class="group1" href="/assets/images/submission/mag-e.jpg" title="Submission of metagenome assembly data"> <figure class="image"> <img src="/assets/images/submission/mag-e.jpg" alt="Submission of metagenome assembly data" class="w600" /> <figcaption>Submission of metagenome assembly data</figcaption> </figure> </a> </div> <h3 id="raw-reads">(1) Raw reads</h3> <p>Unassembled raw sequence data should be submitted to <a href="/dra/submission-e.html">DRA Run</a>.</p> <h4 id="raw-reads-bioproject">BioProject</h4> <p>Register your BioProject as a <a href="/bioproject/project-info-e.html#Project-type">metagenome/environmental project</a>. For the organism name, choose the most appropriate “xyz metagenome” (e.g., soil metagenome) from this list of <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&keep=1&srchmode=3&unlock/">metagenome organism names</a> in the taxonomy database.</p> <h4 id="raw-reads-biosample">BioSample</h4> <p>Register your BioSample by using the <a href="/biosample/sample-info-e.html#mixs">MIxS MIMS.me</a> package. For the organism name, choose the most appropriate “xyz metagenome” (e.g., soil metagenome) from this list of <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&keep=1&srchmode=3&unlock/">metagenome organism names</a> in the taxonomy database. Please provide as much metadata and information as possible about the samples in order to provide context for the experimental data.</p> <h4 id="raw-reads-dra">DRA</h4> <p>Submit unassembled raw sequence data to <a href="/dra/submission-e.html">DRA Run</a>.</p> <h3 id="primary-metagenome">(2) Primary metagenome</h3> <p>Assembled contigs derived from the raw sequence data should be submitted to <a href="/dra/submission-e.html">DRA Analysis</a>.</p> <h4 id="primary-metagenome-bioproject">BioProject</h4> <p>Same as (1) Raw reads.</p> <h4 id="primary-metagenome-biosample">BioSample</h4> <p>Same as (1) Raw reads.</p> <h4 id="primary-metagenome-dra">DRA</h4> <p>Submit assembled contigs derived from the raw sequence data in fasta/bam files to the <a href="/dra/metadata-e.html#Analysis_Type">DRA Analysis</a> (Analysis type = ‘De Novo Assembly’) along with the Run registered in (1). By using <a href="/dra/submission-e.html#excel">the excel for DRA submission</a>, describe analysis software used in Analysis step and quality metrics in Attributes. <br /> If using the DRA submission web interface, include information of a referencing BioSample accession, analysis software used and assembly quality metrics in the description.</p> <ul> <li>BioSample: SAMD00000001</li> <li>Analysis step: canu 2.1, pilon 1.24, CheckM 1.1.3</li> <li>Quality: completeness 85.3, contamination 0</li> </ul> <p>Please note that Analysis data are not shared with NCBI/ENA. Analysis is not indexed by <a href="https://ddbj.nig.ac.jp/search">DDBJ Search</a>. Only analysis metadata XML and data files are provided in ftp. (For example, <a href="https://ddbj.nig.ac.jp/public/ddbj_database/dra/fastq/DRA000/DRA000072/">DRZ000001</a>.</p> <h3 id="binned-metagenome">(3) Binned metagenome</h3> <p>Binned metagenome assemblies derived from a subset of the raw sequence data should be submitted to <a href="/dra/submission-e.html">DRA Analysis</a>.</p> <h4 id="binned-metagenome-bioproject">BioProject</h4> <p>Same as (1) Raw reads.</p> <h4 id="binned-metagenome-biosample">BioSample</h4> <p>Register a virtual BioSample by using the <a href="/biosample/sample-info-e.html#mixs">“MIMAG”</a> package. Describe an organism name without ‘uncultured’ (e.g., “Agrobacterium tumefaciens”, “Agrobacterium sp.”, “Rhizobiaceae bacterium”) in the taxonomy database from which the binned assembly was derived. Please note that a virtual BioSample derived from the MIMS metagenomic sample used in (1) is required for a binned submission.</p> <p>Among organism names assigned by <a href="https://gtdb.ecogenomic.org/">GTDB</a>, please convert ones not registered in <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi">NCBI Taxonomy</a> to corresponding NCBI Taxonomy’s names.</p> <p>Please describe following attributes to show sample source.</p> <p>Describe metagenome source in metagenome_source by using one of <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&keep=1&srchmode=3&unlock/">metagenome organism names</a>. Example) metagenome_source: soil metagenome</p> <p>Indicate derived metagenome sample registered in (1) by entering BioSample accession(s) in derived_from. Example) derived_from: SAMD00000001 derived_from: SAMD00000002,SAMD00000003,SAMD00000010-SAMD00000015</p> <h4 id="binned-metagenome-dra">DRA</h4> <p>Submit binned assemblies derived from the raw sequence data in fasta/bam files to the <a href="/dra/metadata-e.html#Analysis_Type">DRA Analysis</a> (Analysis type = ‘De Novo Assembly’) along with the Run registered in (1). By using <a href="/dra/submission-e.html#excel">the excel for DRA submission</a>, describe analysis software used in Analysis step, and quality metrics and binning information in Attributes. <br /> If using the DRA submission web interface, include information of a referencing BioSample accession, analysis software used, and assembly quality metrics and binning information in the description.</p> <ul> <li>BioSample: SAMD00000001</li> <li>Analysis step: canu 2.1, pilon 1.24, CheckM 1.1.3</li> <li>Quality: completeness 85.3, contamination 0</li> </ul> <p>Please note that Analysis data are not shared with NCBI/ENA. Analysis is not indexed by <a href="https://ddbj.nig.ac.jp/search">DDBJ Search</a>. Only analysis metadata XML and data files are provided in ftp. (For example, <a href="https://ddbj.nig.ac.jp/public/ddbj_database/dra/fastq/DRA000/DRA000072/">DRZ000001</a></p> <h3 id="mag">(4) MAG</h3> <p>Metagenomic assemblies (Metagenome-Assembled Genomes, MAGs) predicted to be derived from taxonomically defined organisms should be submitted to DDBJ as genome entries of <a href="/ddbj/env-e.html">ENV division</a>.</p> <h4 id="mag-bioproject">BioProject</h4> <p>Register your BioProject as a <a href="/bioproject/project-info-e.html#Project-type">metagenome/environmental project</a>. If you have already registered a BioProject for submission of the corresponding raw reads to DRA, then, in general, you would use the BioProject when you submit the MAG to DDBJ.</p> <h4 id="mag-biosample">BioSample</h4> <p>Register a virtual BioSample by using the <a href="/biosample/sample-info-e.html#mixs">“MIMAG”</a> package. Describe an organism name without ‘uncultured’ (e.g., Agrobacterium tumefaciens) in the taxonomy database from which the MAG was derived. Please note that a virtual BioSample derived from the MIMS metagenomic sample used in (1) is required for a MAG submission.</p> <p>Among organism names assigned by <a href="https://gtdb.ecogenomic.org/">GTDB</a>, please convert ones not registered in <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi">NCBI Taxonomy</a> to corresponding NCBI Taxonomy’s names.</p> <p>Please describe following attributes to show sample source.</p> <p>Describe metagenome source in metagenome_source by using one of <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&keep=1&srchmode=3&unlock/">metagenome organism names</a>. Example) metagenome_source: soil metagenome</p> <p>Indicate derived metagenome sample registered in (1) by entering BioSample accession(s) in derived_from. Example) derived_from: SAMD00000001 derived_from: SAMD00000002,SAMD00000003,SAMD00000010-SAMD00000015</p> <p><a href="https://docs.google.com/spreadsheets/d/1VCCuSwvIRfp5-DT8cnvvAwWH4C7wbDFSjHQ_q3f3BII/edit#gid=272411182">Example BioSample</a></p> <h4 id="mag-dra">DRA</h4> <p>The raw sequence data used for the MAG assembly should be submitted to the DRA Run.</p> <h4 id="mag-ddbj">DDBJ</h4> <p>Submit the MAG as a genome entry of <a href="/ddbj/env-e.html">ENV division</a> through the <a href="/ddbj/mss-e.html">Mass Submission System (MSS)</a>. Following <a href="/ddbj/qualifiers-e.html">Qualifier</a> of <a href="/ddbj/features-e.html#source">source feature</a> are required for the MAG submission.</p> <p>Required for the MAG entry.</p> <ul> <li><a href="/ddbj/qualifiers-e.html#metagenome_source">/metagenome_source</a> = ‘xyz metagenome’ (‘xyz metagenome’ should be from this list of <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&keep=1&srchmode=3&unlock/">metagenome organism names</a> in the taxonomy database).</li> </ul> <p>Required for the ENV division entry.</p> <ul> <li><a href="/ddbj/qualifiers-e.html#environmental_sample">/environmental_sample</a></li> <li><a href="/ddbj/qualifiers-e.html#isolation_source">/isolation_source</a></li> <li><a href="/ddbj/qualifiers-e.html#isolate">/isolate</a></li> </ul> <p>Required for All entry.</p> <ul> <li><a href="/ddbj/organism-e.html#MAG">/organism</a></li> <li><a href="/ddbj/qualifiers-e.html#mol_type">/mol_type</a> = “genomic DNA”</li> </ul> <p>The assebly information is necessary in <a href="/ddbj/file-format-e.html#describing_st_comment">ST_COMMENT</a> as a genome entry.</p> <ul> <li>Assembly Method</li> <li>Genome Coverage</li> <li>Sequencing Technology</li> <li>Assembly Name (required in the case of eukaryotes)</li> </ul> <p>In the MAG (ENV division) entry, <a href="/ddbj/qualifiers-e.html#strain">/strain</a> can not be used. <br /> Please describe natural host of the organism from which sequenced molecule was obtained in /host.</p> </main> </section> </div> </section> </div> <footer></footer> <div id="back-top"></div> </body> </html>