Metaphlan results as input on Humann

Microbial community profiling HUMAnN
1

Hi dears,
For some reasons, all my metagenome data had generated firstly by Metaphlan and now I want to run with humann. I browsed forum and found some related topics like:

  1. Humann 3.0 and bowtie metaphlan output
  2. Input Specification if Pre-Existing MetaPhlAn Files
  3. Question about using MetaPhlAn3 output as input for HUMAnN3

I had bowtie & sam files from metaphlan and the I used

humann -i $sample_sam -o $sample_out --threads 45 --taxonomic-profile $sample_metaphlan.txt --input-format sam

generated results with something like “UNMAPPED 0.0000000000 UNINTEGRATED 0.0000000000”

Now I have to run humann with raw input fasta file. So the bowtie & sam files from metaphlan have not useful for humann in any way？

Sincerely,

Louie

2

If you’ve already run MetaPhlAn on your samples you can skip that step in HUMAnN by passing the existing taxonomic profile to HUMAnN via the --taxonomic-profile flag. You would pass your input reads and specify an output folder as normal.

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