[ ソース: metaphlan ]
パッケージ: 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
その他の metaphlan 関連パッケージ
|
|
|
|
-
- dep: bowtie2
- ultrafast memory-efficient short read aligner
-
- dep: metaphlan2-data
- data package for Metagenomic Phylogenetic Analysis
-
- dep: python3
- interactive high-level object-oriented language (default python3 version)
-
- dep: python3-biom-format
- Biological Observation Matrix (BIOM) format (Python 3)
-
- dep: python3-biopython
- Python3 library for bioinformatics
-
- dep: python3-dendropy
- DendroPy Phylogenetic Computing Library (Python 3)
-
- dep: python3-msgpack
- Python 3 implementation of MessagePack format
-
- dep: python3-numpy
- Fast array facility to the Python language (Python 3)
-
- dep: python3-pandas
- data structures for "relational" or "labeled" data
-
- dep: python3-pysam
- interface for the SAM/BAM sequence alignment and mapping format (Python 3)
-
- dep: python3-requests
- 人間のために作られた、Python 3 向けの洗練された単純な HTTP ライブラリ
-
- dep: python3-scipy
- scientific tools for Python 3