Qiime-compatible taxonomic databases with species information

[Carla_Uranga]

Hi, does the silva-138-99-seqs.qza database contain species-level taxonomic information? Is it possible to use the headers in a custom fasta file as a taxonomy.tsv file, and if so, what are the parsing rules? Thanks.

[Nicholas_Bokulich]

Hi @Carla_Uranga,

@Carla_Uranga

does the silva-138-99-seqs.qza database contain species-level taxonomic information?

Yes — as with other QIIME 2 artifacts, you can check out the provenance to confirm the processing steps, and since this artifact was generated with RESCRIPt, the SILVA taxonomy parsing steps are recorded in provenance:

@Carla_Uranga

Is it possible to use the headers in a custom fasta file as a taxonomy.tsv file

I'm not 100% sure what you mean, but yes in theory you can include any kind of annotation information, including sequence IDs, in a taxonomy file.

@Carla_Uranga

and if so, what are the parsing rules?

The taxonomy files used by QIIME 2 consist of TSVs in this format:
feature IDsemicolon;delimited;taxonomy;annotation

So you can make a custom database of any kind, so long as it conforms to that format.

Good luck!