Dataset Open Access

Nematode ITS2 Database

Workentine, Matthew

Nematode ITS2 database

These are the sequence and taxonomy files for the Nematode ITS2 database.  This database was created with markerDB. Please see that repository for full details on the file formats.  The main database consists of the "seqs_nr.fasta" and the associated "taxonomy_nr.txt".  These contain the non-redundant ITS2 sequences.

The database is available in some other common formats used for assigning taxonomy and are listed below.

  • dada2: dada2’s assignTaxonomy function
  • rdp: to train a custom RDP database with the rRDP Bioconductor package (this is pretty much the same as assignTaxonomy)
  • mothur: a fasta file and paired mothur taxonomy file. Works with the Nemabiome pipeline. An alignment is also written out that should work with mothur, but can also be used for other pipelines as needed.
  • idtaxa: a fasta file and taxonomy file for IDTAXA.

Files (72.3 MB)
Name Size
Nematode_ITS2_1.0.0_dada2.fasta
md5:b92cb6f5ff898379a04f585eab3951fb
3.4 MB Download
Nematode_ITS2_1.0.0_db_info.txt
md5:cb167c776559e1a4621d375380262042
131 Bytes Download
Nematode_ITS2_1.0.0_idtaxa.fasta
md5:1973f2799a08b960968af01952c6df8e
3.4 MB Download
Nematode_ITS2_1.0.0_idtaxa.tax
md5:7fb8601b17a2ca4631b94b154e18c49a
71.1 kB Download
Nematode_ITS2_1.0.0_mothur.aln
md5:db577dc246688c836c9d0b18ad67b79e
54.5 MB Download
Nematode_ITS2_1.0.0_mothur.fasta
md5:9d8e5d6bb239fd90c3bca004ab6d1dfe
2.6 MB Download
Nematode_ITS2_1.0.0_mothur.tax
md5:88510001f37ec8fb59a1160ec57d9529
963.0 kB Download
Nematode_ITS2_1.0.0_rdp.fasta
md5:ab4958fdbefa5153dedbf536f160ee1b
3.5 MB Download
Nematode_ITS2_1.0.0_seqs_nr.fasta
md5:9d8e5d6bb239fd90c3bca004ab6d1dfe
2.6 MB Download
Nematode_ITS2_1.0.0_taxonomy_nr.txt
md5:084d2918d5783364053c6b27bf33c751
1.1 MB Download
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