strainphlan
Metagenomic Phylogenetic Analysis
Install
- All systems
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curl cmd.cat/strainphlan.sh
- Debian
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apt-get install metaphlan2 - Ubuntu
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apt-get install metaphlan2 - Kali Linux
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apt-get install metaphlan2 - Windows (WSL2)
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sudo apt-get updatesudo apt-get install metaphlan2 - Raspbian
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apt-get install metaphlan2 - Dockerfile
- dockerfile.run/strainphlan
metaphlan2
Metagenomic Phylogenetic Analysis
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species. MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the marker information file can be found at usr/share/metaphlan2/utils/markers_info.txt.bz2) identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 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