Nematode ITS2 Database

<p><strong>Nematode ITS2 database</strong></p> <p>These are the sequence and taxonomy files for the Nematode ITS2 database.&nbsp; This database was created with <a href="https://github.com/ucvm/markerDB">markerDB</a>. Please see that repository for full details on the file formats.&nbsp; The main database consists of the &quot;seqs_nr.fasta&quot; and the associated &quot;taxonomy_nr.txt&quot;.&nbsp; These contain the non-redundant ITS2 sequences.</p> <p>The database is available in some other common formats used for assigning taxonomy and are listed below<code>.</code></p> <ul> <li>dada2: dada2&rsquo;s <code>assignTaxonomy</code> function</li> <li>rdp: to train a custom RDP database with the <code>rRDP</code> Bioconductor package (this is pretty much the same as <code>assignTaxonomy</code>)</li> <li>mothur: a fasta file and paired mothur taxonomy file. Works with the <a href="https://www.nemabiome.ca/">Nemabiome</a> pipeline. An alignment is also written out that should work with mothur, but can also be used for other pipelines as needed.</li> <li>idtaxa: a fasta file and taxonomy file for <a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0521-5">IDTAXA</a>.</li> </ul>