metaphlan

Metagenomic Phylogenetic Analysis

Description

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. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest marker information file mpa_v31_CHOCOPhlAn_201901_marker_info.txt.bz2 can be found here) identified from ~100,000 reference genomes (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:

* unambiguous taxonomic assignments;

* accurate estimation of organismal relative abundance;

* species-level resolution for bacteria, archaea, eukaryotes and

viruses;

* strain identification and tracking

* orders of magnitude speedups compared to existing methods.

* metagenomic strain-level population genomics

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Homepage

https://github.com/biobakery/MetaPhlAn

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