SAMtools

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Attention: Research Computing Documentation has Moved
https://docs.rc.uab.edu/


Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.


As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

This page is a Generic stub.

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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