2019-08-03 01:45:29 +02:00
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MetaPhlAn2 is a computational tool for profiling the composition of
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microbial communities (Bacteria, Archaea and Eukaryotes) from meta-
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genomic shotgun sequencing data (i.e. not 16S) with species-level.
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With the newly added StrainPhlAn module, it is now possible to perform
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accurate strain-level microbial profiling. MetaPhlAn2 relies on ~1.5M
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unique clade-specific marker genes. The latest marker information file
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`mpa_v29_CHOCOPhlAn_201901_marker_info.txt.bz2` can be found in the
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Download page (https://bitbucket.org/biobakery/metaphlan2/downloads/)
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identified from ~100,000 reference genomes (~99,500 bacterial and
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archaeal and ~500 eukaryotic), allowing:
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* unambiguous taxonomic assignments;
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* accurate estimation of organismal relative abundance;
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2020-10-08 22:48:32 +02:00
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* species-level resolution for bacteria, archaea, eukaryotes, viruses;
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2019-08-03 01:45:29 +02:00
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* strain identification and tracking
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* orders of magnitude speedups compared to existing methods.
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* metagenomic strain-level population genomics
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If you use MetaPhlAn2, please cite:
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MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Duy Tin Truong,
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Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart,
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Edoardo Pasolli, Adrian Tett, Curtis Huttenhower & Nicola Segata. Nature
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Methods 12, 902-903 (2015)
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If you use StrainPhlAn, please cite the MetaPhlAn2 paper and the
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following StrainPhlAn paper:
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Microbial strain-level population structure and genetic diversity from
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metagenomes. Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis
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Huttenhower, & Nicola Segata. Genome Research 27:626-638 (2017)
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NOTE!
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The script places the python files in /usr/share/MetaPhlAn2 and creates
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symlinks to /usr/bin. If you are using metaphlan2.py with Ugene, it may
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not work with the symlink. Instead, just point Ugene directly to
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/usr/share/MetaPhlAn2/metaphlan2.py
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