academic/MetaPhlAn2: Added (Metagenomic Phylogenetic Analysis).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 36 insertions, 0 deletions

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+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 and 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