---
name: "paleomix"
section: "1"
platform: "linux"
package: "paleomix"
version: "1.3.8-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/paleomix"
---

# paleomix(1)

pipelines and tools for HTS data analyses

## 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.