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biocore / q2-greengenes2

A QIIME 2 plugin for interaction with the Greengenes2 database
BSD 3-Clause "New" or "Revised" License
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What file(s) on the GG2db ftp site can be used as reference-taxonomy for classification by q2-greengenes2 plugin? #28

Closed VoronDM closed 1 week ago

VoronDM commented 1 week ago

Hi,

I tried to classify my amplicons sequences with q2-greengenes2 plugin. Unsuccessfully.

What file(s) on the ftp can be used for classification using q2-greengenes2 plugin as --i-reference-taxonomy? Do I understand correctly that a file with multiple amplicons sequences (.qza) can be used as input in --i-reads?

$ qiime greengenes2 taxonomy-from-features \ --i-reference-taxonomy \ --i-reads <your_FeatureData[Sequence]> \ --o-classification

Thanks.

wasade commented 1 week ago

Hi @VoronDM, as this relates to QIIME 2, could you please first check the QIIME 2 Forum, and open a thread on there if needed?

The reference taxonomy to use would depend on how your ASVs are expressed and upstream processing. But, if I remember correctly of that input, you could use 2024.09.taxonomy.asv.nwk.qza. The reads would need to be, as noted, a FeatureData[Sequence] artifact.