套件：paleomix（1.3.8-1 以及其他的）
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.
其他與 paleomix 有關的套件
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- dep: adapterremoval
- rapid adapter trimming, identification, and read merging of gene sequences
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- dep: bcftools
- genomic variant calling and manipulation of VCF/BCF files
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- dep: bedtools
- suite of utilities for comparing genomic features
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- dep: bowtie2
- ultrafast memory-efficient short read aligner
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- dep: bwa
- Burrows-Wheeler Aligner
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- dep: examl
- Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
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- dep: mafft
- Multiple alignment program for amino acid or nucleotide sequences
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- dep: mapdamage
- tracking and quantifying damage patterns in ancient DNA sequences
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- dep: phylip
- package of programs for inferring phylogenies
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- dep: picard-tools
- Command line tools to manipulate SAM and BAM files
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-coloredlogs
- colored terminal output for Python 3's logging module
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- dep: python3-configargparse
- replacement for argparse with config files and environment variables
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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-ruamel.yaml
- Roundtrip YAML parser/emitter (Python 3 module)
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- dep: python3-setproctitle
- Setproctitle implementation for Python 3
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- dep: r-base-core
- GNU R core of statistical computation and graphics system
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- dep: radiant
- explore hierarchical metagenomic data with zoomable pie charts
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- dep: raxml
- Randomized Axelerated Maximum Likelihood of phylogenetic trees
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- dep: samtools
- processing sequence alignments in SAM, BAM and CRAM formats