SAMtools: Difference between revisions

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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:
[http://genome.sph.umich.edu/wiki/SAM 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 flexible enough to store all the alignment information generated by various alignment programs;
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*Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.  
*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.
[http://samtools.sourceforge.net/ 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 website:''' http://samtools.sourceforge.net/


Project homepage: http://samtools.sourceforge.net/
====Load SGE module====
 
The following Modules files should be loaded for this package:
The following Modules files should be loaded for this package:
<pre>
<pre>
module load samtools/samtools
module load samtools/samtools
</pre>
</pre>
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]

Latest revision as of 15:37, 4 April 2012

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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 website: http://samtools.sourceforge.net/

Load SGE module

The following Modules files should be loaded for this package:

module load samtools/samtools