[ 原始碼： metaphlan ]
套件：metaphlan（4.0.4-1）
Metagenomic Phylogenetic Analysis
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic 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.
MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest marker information file mpa_v31_CHOCOPhlAn_201901_marker_info.txt.bz2 can be found here) 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
其他與 metaphlan 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: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-biom-format
- Biological Observation Matrix (BIOM) format (Python 3)
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- dep: python3-biopython
- Python3 library for bioinformatics
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- dep: python3-dendropy
- DendroPy Phylogenetic Computing Library (Python 3)
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- dep: python3-msgpack
- Python 3 implementation of MessagePack format
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- dep: python3-numpy
- Fast array facility to the Python language (Python 3)
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- dep: python3-pandas
- data structures for "relational" or "labeled" data
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- dep: python3-pysam
- interface for the SAM/BAM sequence alignment and mapping format (Python 3)
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- dep: python3-requests
- elegant and simple HTTP library for Python3, built for human beings
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- dep: python3-scipy
- scientific tools for Python 3