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Contents of README:MetaPhlAn2 is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from meta- genomic 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. MetaPhlAn2 relies on ~1.5M unique clade-specific marker genes. The latest marker information file `mpa_v29_CHOCOPhlAn_201901_marker_info.txt.bz2` can be found in the Download page (https://bitbucket.org/biobakery/metaphlan2/downloads/) 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, viruses; * strain identification and tracking * orders of magnitude speedups compared to existing methods. * metagenomic strain-level population genomics If you use MetaPhlAn2, please cite: MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Duy Tin Truong, Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower & Nicola Segata. Nature Methods 12, 902-903 (2015) If you use StrainPhlAn, please cite the MetaPhlAn2 paper and the following StrainPhlAn paper: Microbial strain-level population structure and genetic diversity from metagenomes. Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, & Nicola Segata. Genome Research 27:626-638 (2017) NOTE! The script places the python files in /usr/share/MetaPhlAn2 and creates symlinks to /usr/bin. If you are using metaphlan2.py with Ugene, it may not work with the symlink. Instead, just point Ugene directly to /usr/share/MetaPhlAn2/metaphlan2.py |
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Parent Directory - 4e4416321c75828ac8ea55d36f5a65ebd39058c5.tar.gz 03-Jun-2022 13:33 34M MetaPhlAn2.SlackBuild 11-Mar-2022 06:34 3.0K MetaPhlAn2.info 03-Jun-2022 13:32 475 README 03-Jun-2022 13:32 1.8K References 03-Jun-2022 13:32 707 slack-desc 03-Jun-2022 13:32 1.0K
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