PALEOMIX(1)

NAME
paleomix - pipelines and tools for HTS data analyses

SYNOPSIS
paleomix <command> [options]

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.

OPTIONS

  Pipelines

paleomix bam_pipeline
    Pipeline for trimming and mapping of NGS reads.

paleomix trim_pipeline
    Equivalent to 'bam_pipeline', but only runs the trimming steps.

paleomix phylo_pipeline
    Pipeline for genotyping and phylogenetic inference from BAMs.

paleomix zonkey
    Pipeline for detecting F1 (equine) hybrids.

  BAM/SAM tools:

paleomix cleanup
    Reads SAM file from STDIN, and outputs sorted, tagged, and filter BAM, for which NM and MD tags have been updated.

paleomix coverage
    Calculate coverage across reference sequences or regions of interest.

paleomix depths
    Calculate depth histograms across reference sequences or regions of interest.

paleomix duphist
    Generates PCR duplicate histogram; used with the 'Preseq' tool.

paleomix rmdup_collapsed
    Filters PCR duplicates for collapsed pairedended reads generated by the AdapterRemoval tool.

  VCF/GTF/BED/Pileup tools:

paleomix genotype
    Creates bgzipped VCF for a set of (sparse) BED regions, or for entire chromosomes / contigs using SAMTools / BCFTools.

paleomix gtf_to_bed
    Convert GTF file to BED files grouped by feature (coding, RNA, etc).

paleomix sample_pileup
    Randomly sample sites in a pileup to generate a FASTA sequence.

paleomix vcf_filter
    Quality filters for VCF records, similar to 'vcfutils.pl varFilter'.

paleomix vcf_to_fasta
    Create most likely FASTA sequence from tabixindexed VCF file.

  Misc tools:

paleomix cat
    Generalized cat command for gz, bz2 and uncompressed files.

AUTHOR
If you make use of PALEOMIX in your work, please cite

    Schubert et al, "Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX". Nature Protocols. 2014 May; 9(5): 1056-82. doi: 10.1038/nprot.2014.063

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.