[ 原始碼： metaphlan2 ]
套件：metaphlan2（2.7.8-1）
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
其他與 metaphlan2 有關的套件
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- dep: bowtie2
- ultrafast memory-efficient short read aligner
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- dep: metaphlan2-data
- data package for Metagenomic Phylogenetic Analysis
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- dep: python
- interactive high-level object-oriented language (Python2 version)
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- dep: python-biom-format
- Biological Observation Matrix (BIOM) format (Python 2)
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- dep: python-msgpack
- Python implementation of MessagePack format
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- dep: python-pandas
- data structures for "relational" or "labeled" data