Taxonomy classification using SILVA 138

Hello,

We need to perform taxonomy classification of gut microbiome data V4/16S using qiime and silva 138.

Which command do we have to use to perform classification noting that we have rep-seqs.qza file ?

How can we generate output data related to Archae and bacteria separately ?

Thanks

HI @M_F,

You can follow the examples contained within the Jupyter Book Tutorials, namely this example. You can also see the corresponding steps as outlined in any of the other online tutorials.

If you use SILVA, GTDB, RDP... see the RESCRIPt tutorials or even the Greengenes2 tutorial. Both the Archaea and Bacteria will be classified. You can filter / subset into Bacterial and Archaeal sequences & tables post classification as per these instructions.