Paket: metaphlan (4.0.4-1)

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Externa resurser:

Hemsida [github.com]

Liknande paket:

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

Andra paket besläktade med metaphlan

beror

rekommenderar

föreslår

enhances

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 3 language
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

elegant and simple HTTP library for Python3, built for human beings
dep: python3-scipy

scientific tools for Python 3

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