UNITE/QIIME 12_11 ITS reference OTUs now available (alpha release!)

27 11 2012

Hi all,

I’m pleased to announce that as part of a collaborative effort we have released the 12_11 alpha version of the UNITE/QIIME ITS reference OTUs. These are now linked from the QIIME resources page. These can be used for open or closed reference OTU picking, and for assigning taxonomy to ITS reads. Taxonomy can be assigned using BLAST in QIIME 1.5.0, or BLAST and RDP in QIIME 1.5.0-dev (and in the coming 1.6.0 release). See the acknowledgements list for the list of those involved.

The 12_11 release should be considered an alpha release, meaning that it is a very early stage release and errors are certain to exist. You should interpret results with care. We are releasing this now to provide tools to better support ITS analysis in QIIME, and we’ll be improving these OTUs over time. These are derived from the UNITE database (UNITE_public_24.09.12 release). You can find details on how these were created in the README.md file packaged with the release. Efforts have been made by UNITE to improve the taxonomic information associated with some of the sequences in their database. The QIIME reference sequence sets linked here have not been subject to any other form of curation (manual or automated) and certainly include incorrectly identified taxonomy, chimeras, and other problematic sequences. Improved fungal rDNA ITS reference sets based on the semi-curated centroids for sequence clusters in the UNITE Global Key Annotations module will soon be available from the QIIME resources page.

Please direct any feedback (either issues that you notice or feature requests) to the its-reference-otus issue tracker on GitHub, and direct any questions to the QIIME Forum. All files are additionally available in the its-reference-otus GitHub repository

You can use these files in the same way as you would use the Greengenes reference OTUs, just substituting files from this data set as the reference sequences and taxonomy.

This collaboration arose from the Sloan Foundation‘s Fungal ITS Workshop held on 19–20 October, 2012 in Boulder, Colorado, USA.

Enjoy!

Greg

 

 

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