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/ | |||
====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