MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.

Profile Format

Taxpasta expects a four-column, tab-separated file. This is generated by redirecting the MetaPhlAn3 stdout. It interprets the columns as:

Column Header	Description
clade_name
taxonomy_id
relative_abundance1
additional_species

Example

#mpa_v30_CHOCOPhlAn_201901
#/workspace/nextflow-mentoring/second_pipeline/work/conda/env-e9a987b33d7e880200ff2190a27ad05d/bin/metaphlan ERR525939.trimmed.R1.fastq.gz,ERR525939.trimmed.R2.fastq.gz --bowtie2out metagenome.bowtie2.bz2 --input_type fastq -o ERR525939.taxa.txt
#SampleID   Metaphlan_Analysis
#clade_name NCBI_tax_id relative_abundance  additional_species
k__Bacteria 2   100.0
k__Bacteria|p__Bacteroidetes    2|976   65.30411
k__Bacteria|p__Proteobacteria   2|1224  27.81459
k__Bacteria|p__Firmicutes   2|1239  4.35836

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1. Value used in standardised profile output, multiplied with a fixed number to yield an integer for the standardised profile ↩