HUMAnN - Pathway contribution data

Microbial community profiling HUMAnN
1

Do you have any suggestions for generating pathway contribution data with results similar to a picrust2 run? I’ve attached a sample file.

For the picrust2 run, I used the following command line:

pathway_pipeline.py \
  -i KO_metagenome_out/pred_metagenome_unstrat.tsv.gz \
  -o pathway_contrib \
  --per_sequence_contrib \
  --per_sequence_abun KO_metagenome_out/seqtab_norm.tsv.gz \
  --per_sequence_function KO_predicted.tsv.gz \
  --no_regroup \
  --map pathway_gene_map.tsv

Thanks in advance.

path_con_example.csv (1.0 KB)

2

If the key detail here is getting from predicted KO abundances (via PICRUSt) to KEGG pathways, you can generate metagenome-inferred KO abundances from HUMAnN by regrouping your genefamilies.tsv output to KOs using the regroup_table function.

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