Pavian with amplicon sequencing data

[slambrechts]

Hi,

Is there a way to use Pavian with amplicon sequencing data (e.g. 16S or 18S)?

Best,
Sam

[MaryoHg]

You need to convert you taxonomic information into pavian formats, e.g., kraken, mpa of centrifuge format.
I'm into it and I can't seem to resolve how to convert either phyloseq-object or OTU-table to a mpa-style file.

Good luck. I hope you solved it already.