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MetaPhlAn

Profiles the composition of microbial communities from metagenomic shotgun sequencing data

https://github.com/biobakery/MetaPhlAn

The module supports outputs from MetaPhlAn, that look like the following:

k__Bacteria	2	100.0
k__Bacteria|p__Firmicutes	2|1239	44.30422
k__Bacteria|p__Bacteroidetes	2|976	34.73101

A bar graph is generated that shows the relative abundance for each sample that fall into the top-10 categories for each taxa rank. The top categories are calculated by summing the relative abundances across all samples.

Any species under the Additional Species column are ignored when making the graphs.

The number of top categories to plot can be customized in the config file:

metaphlan:
  top_n: 10

File search patterns​

metaphlan:
  contents: "#clade_name\tNCBI_tax_id\trelative_abundance\t"
  fn: "*.txt"