Package: paleomix (1.2.13.3-1)

[ Source: paleomix  ]

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.

Other Packages Related to paleomix

• 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 (Python2 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, BAM and CRAM formats

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