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Пакет: paleomix (1.2.12-1)

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paleomix

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pipelines and tools for the processing of ancient and modern HTS data

The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts.

The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing.

Други пакети, свързани с paleomix

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  • препоръчани
  • предложени
  • dep: adapterremoval
    rapid adapter trimming, identification, and read merging of gene sequences
  • dep: bcftools
    genomic variant calling and manipulation of VCF/BCF files
  • dep: bedtools
    suite of utilities for comparing genomic features
  • dep: bowtie2
    ultrafast memory-efficient short read aligner
  • dep: bwa
    Burrows-Wheeler Aligner
  • dep: examl
    Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
  • dep: mafft
    Multiple alignment program for amino acid or nucleotide sequences
  • dep: mapdamage
    tracking and quantifying damage patterns in ancient DNA sequences
  • dep: phylip
    package of programs for inferring phylogenies
  • dep: picard-tools
    Command line tools to manipulate SAM and BAM files
  • dep: python
    interactive high-level object-oriented language (default version)
  • dep: python-coverage
    code coverage tool for Python 2
  • dep: python-flexmock
    Mock/Stub/Spy library for Python
  • dep: python-pysam
    interface for the SAM/BAM sequence alignment and mapping format (Python 2)
  • dep: python-setproctitle
    Setproctitle implementation for Python 2
  • dep: r-base-core
    GNU R core of statistical computation and graphics system
  • dep: radiant
    explore hierarchical metagenomic data with zoomable pie charts
  • dep: raxml
    Randomized Axelerated Maximum Likelihood of phylogenetic trees
  • dep: samtools
    processing sequence alignments in SAM and BAM formats

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