bam_pipeline - BAM pipeline of PALEOMIX suite
bam_pipeline [
options]
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.
bam_pipeline is the BAM pipeline of
paleomix(1).
- bam_pipeline help
- Display this message
- bam_pipeline example [...]
- Create example project in folder.
- bam_pipeline makefile [...]
- Print makefile template.
- bam_pipeline dryrun [...]
- Perform dry run of pipeline on provided makefiles.
Equivalent to 'bam_pipeline run --dry-run [...]'.
- bam_pipeline run [...]
- Run pipeline on provided makefiles.
- bam_pipeline remap [...]
- Re-map hits from previous alignment.
paleomix(1)
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.