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.