paleomix
pipelines and tools for the processing of ancient and modern HTS data
Command lineScience
Not tested on a device yet. What that means
Commands in the package
paleomix
About paleomix
From Debian's package description
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.
From Debian's description of the paleomix package, under that package's license.
Dependencies
Depends on
python3-coloredlogspython3-configargparsepython3-pysampython3-ruamel.yamlpython3-setproctitlepython3adapterremovalbedtoolsbowtie2bwabcftoolsexamlmafftmapdamagephylippicard-toolsr-base-coreradiantraxmlsamtools
Related apps
- ea-utilscommand-line tools for processing biological sequencing dataCommand line
- open3d-toolsLibrary for 3D data processing - toolsCommand line
- SatDumpGeneric satellite data processing software
- subreadtoolkit for processing next-gen sequencing dataCommand line
- mapdamagetracking and quantifying damage patterns in ancient DNA sequencesCommand line
- weightwatcherCombine maps and polygon data for astronomical image processingCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the paleomix package, under that package's license.
- Description: Debian's description of the paleomix package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.