SAMtools
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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.
Project homepage: http://samtools.sourceforge.net/
The following Modules files should be loaded for this package:
module load samtools/samtools