Filtering Alignment Results for Fungi in PlusPF Database

[anzhi525]

"I have already downloaded the PlusPF database from https://benlangmead.github.io/aws-indexes/k2. This database includes Refeq archaea, bacteria, viral, plasmid, human1, UniVec_Core, protozoa & fungi. I want to output only the alignment results for fungi. How should I proceed?"

[smdabdoub]

I would suggest using kraken-biom to convert your output report files to a BIOM table, then import into phyloseq where you can filter based on taxa:

GP.chl = subset_taxa(GlobalPatterns, Phylum=="Chlamydiae")