Generate pathabundance and pathcoverage only

Microbial community profiling HUMAnN
1

I do know this command will produce three files, including genefamilies, pathabundance and pathcoverage

$ humann --input $SAMPLE --output $OUTPUT_DIR

I was wondering if I can produce pathabundance and pathcoverage only without genefamilies.
I was used the previous version of database, including uniprot, metacyc, mapping file, to perform the analysis. However, comparing uniprot annotation 2019 with 2019b, both files are exactly the same.
Therefore I don’t want to spend the time for producing genefamilies again.

Is it possible?

2

Hello, Yes you can. If you provide your prior gene families file as input to humann it will start with the gene families and just generate the two pathways files; This like you said will reduce the compute time considerably because both the nucleotide and translated search portions don’t need to be run with the gene families file used as input.

Thanks!
Lauren