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MetaPhlAn2 (version 2.6.0.1)

Input file:

Database with clade-specific marker genes:

Cached database with clade-specific marker genes:

Type of analysis to perform:

Taxonomic level for the relative abundance output:

Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances:

Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded.:

Profile viral organisms?:

Profile eukaryotic organisms?:

Profile bacteria organisms?:

Profile archea organisms?:

Quantile value for the robust average:

What it does

MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the user manual.

Inputs

Metaphlan2 takes as input a sequence file in Fasta, FastQ, a SAM file.

It is also possible to use a custom database with clade-specific marker genes. In this case, a fasta file with marker gene sequences is required and also a file containing metadata. This file is a json file with:

{
  "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
          }
          ...
      }
}

The marker name correspond to the corresponding sequence name in the FastA file containing marker gene sequences.

Outputs

The main output file is a tab-separated file with the predicted taxon relative abundances.