Provided by: paleomix_1.2.12-1_all 
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.