Samtools mpileup (supporting parallelization)

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:

Is flexible enough to store all the alignment information generated by various alignment programs; Is simple enough to be easily generated by alignment programs or converted from existing alignment formats; Is compact in file size; Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory; Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

SAMtools is hosted by SourceForge.net. The project page is http://samtools.sourceforge.net/. The source code releases are available from the download page. You can check out the most recent source code from the github project page with: git clone git://github.com/samtools/samtools.git https://github.com/mydatascience/parallel-mpileup/

Because samtools does not support parallization of the mpileup command, the project was forked to include paralellization support:

However, since the project seems to lack support and contains fatal bugs this project was forked at: https://github.com/yhoogstrate/parallel-mpileup/

Input formats

Satmools accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: "database: hg19" for a link to hg19, or "database: ?" if the link is missing.

Installation

The installation is fully automatic.

License

• parallel-mpileup: MIT License (https://github.com/yhoogstrate/parallel-mpileup/blob/master/samtools-0.1.19/COPYING)
• samtool: MIT License