Question: How to krona plot from easy-taxonomy

[AmaliT]

Hi

I have run mmseqs easy-taxonomyon my query sequences using the nrdatabase and now am keen to generate krona plot using mmseqs taxonomyreport. However I am a bit unsure on what I feed as resultDB for the tanomyreportmodule. Are you able to advise me on this. Thanks in advance

#workflow used
mmseqs databases NR ncbi_nr tmp 
mmseqs easy-taxonomy 00.rawdata/ccs.fasta 00.rawdata/M1.ccs.fasta ncbi_nr mmseq2_analysis/results tmp

[milot-mirdita]

You have to specify the --report-mode 1 parameter to generate Krona output.

Splitting easy-taxonomy up makes generating both outputs at the same time easier:

mmseqs createdb 00.rawdata/ccs.fasta 00.rawdata/M1.ccs.fasta qdb
mmseqs taxonomy qdb ncbi_nr mmseq2_analysis/results tmp
mmseqs taxonomyreport ncbi_nr mmseq2_analysis/results  mmseq2_analysis/results_kraken --report-mode 0
mmseqs taxonomyreport ncbi_nr mmseq2_analysis/results  mmseq2_analysis/results_krona.html --report-mode 1

easy-taxonomy does a bunch additional output files that are slightly more difficult to replicate, however if you only need these two, i'd use this.