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[ 原始碼: metaphlan2  ]

套件: metaphlan2 (2.7.5-1ubuntu1)

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
 * 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

  • 依賴
  • 推薦
  • 建議
  • dep: bowtie2
    ultrafast memory-efficient short read aligner
  • dep: metaphlan2-data
    data package for Metagenomic Phylogenetic Analysis
  • dep: python
    interactive high-level object-oriented language (default version)
  • dep: python-biom-format
    Biological Observation Matrix (BIOM) format (Python 2)
  • dep: python-msgpack
    Python implementation of MessagePack format
  • dep: python-pandas
    data structures for "relational" or "labeled" data

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