What it does

HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.

Read more about the tool: http://huttenhower.sph.harvard.edu/humann2/manual.

This tool corresponds to the main tool in HUMAnN2 pipeline.

Inputs

The input is a single file corresponding either to filtered shotgun sequencing metagenome file (fastq, fastq.gz, fasta, or fasta.gz format), alignment file (sam, bam or blastm8 format) or gene table file (tsv or biom format).

A file with a taxonomic profile (obtained with MetaPhlan2) can also be provided to avoid first step of taxonomic profiling needed to select pangenomes in protein database. Otherwise, default MetaPhlAn2 or custom databases can be used for taxonomic profiling. For custom databases, a fasta file with marker gene sequences is required and also a json file containing metadata:

{
  "taxonomy": {
          "taxonomy of genome1": genome1_length,
          "taxonomy of genome2": genome2_length,
          ...
      }
  "markers": {
          "marker1_name": {
              "clade": the clade that the marker belongs to,
              "ext": [list of external genomes where the marker appears],
              "len": length of the marker,
              "score": score of the marker,
              "taxon": the taxon of the marker
          }
          ...
      }
}

For functional profiling, HUMAnN2 uses multiple databases. Locally cached nucleotide or protein databases have to be downloaded database before using them (using the dedicated tool). Custom databases can also be used after upload. Nucleotide database have to be provided as a dataset.

Outputs

HUMAnN creates three output files:

• A file with gene families and their abundance
• A file with pathways and their abundance
• A file with pathways and their coverage