Announcing the release of a QIIME-formatted version of the SILVA 111 reference database.

25 06 2013

We’re please to announce the availability of a QIIME-formatted version of the SILVA 111 reference database. The aligned SILVA 111 SSU Ref fasta export (SSURef_111_tax_silva_full_align_trunc.fasta.tgz) was downloaded from SILVA (Quast et al 2013; This file was filtered and then clustered into OTUs at  99, 97, 94, and 90 percent similarity within QIIME using UCLUST. Included are OTU maps, taxonomy mapping files, aligned and unaligned reference sequences.  Trees are included only for eukaryotes (18s) as many people may choose to use a different resource, such as the Greengenes reference OTUs, for bacteria and archaea (16S).  Thus, representative set and taxonomy files that only contain eukaryotes (18S) are included in this release. For more detail on reference file generation please see the included notes file (SILVA_111_QIIME_format_notes.txt).

You can download this reference collection from here: QIIME-Silva-111.

Laura Wegener Parfrey




%d bloggers like this: