Get a taxonomy table

[kassammohamed]

Dear all,

I have tried to use MMSEQ taxonomy option with NR data against spades contigs and it works.
Now I would like to create a taxonomy table with reads number like a diamond mapping LCA method against the contigs.
Does someone have tried it?

[milot-mirdita]

We have the module taxonomyreport that builds a Kraken compatible report file. I am not sure what Diamond does, I would have to look that up. Does taxonomyreport already fit your use-case?

See: https://github.com/soedinglab/MMseqs2/wiki#taxonomy-report-in-kraken-or-krona-style