Humann2 input tsv file format

Microbial community profiling HUMAnN
1

Hi there,

Very much a beginner. I have a tsv file of my read counts from whole genome sequencing (see below).

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How can I use this tsv file with humann2 to produce my pathway data?

Thanks,

2

HUMAnN is designed for quantifying pathways from shotgun metagenomic sequencing data (starting from raw reads). If you’re working with sequenced genomes, you might try something like MetaCyc’s Pathway Tools to assign pathways to the genome(s):