SAMtools - Revision history

Tanthony@uab.edu: added category bioinformatics NGS

2012-04-04T15:37:19Z

added category bioinformatics NGS

← Older revision		Revision as of 15:37, 4 April 2012
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	</pre>		</pre>

	[[Category:Software]]		[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]

Tanthony@uab.edu: added category software

2012-04-04T14:15:47Z

added category software

← Older revision		Revision as of 14:15, 4 April 2012
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	module load samtools/samtools		module load samtools/samtools
	</pre>		</pre>

			[[Category:Software]]

Tanthony@uab.edu at 19:53, 2 April 2012

2012-04-02T19:53:41Z

← Older revision		Revision as of 19:53, 2 April 2012
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	'''Project website:''' http://samtools.sourceforge.net/		'''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>

Tanthony@uab.edu at 18:51, 2 April 2012

2012-04-02T18:51:51Z

← Older revision		Revision as of 18:51, 2 April 2012
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	[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.		[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/

	The following Modules files should be loaded for this package:		The following Modules files should be loaded for this package:

Tanthony@uab.edu: added links

2012-03-19T17:04:03Z

added links

← Older revision		Revision as of 17:04, 19 March 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:		[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.

Tanthony@uab.edu at 15:34, 19 March 2012

2012-03-19T15:34:59Z

← Older revision		Revision as of 15:34, 19 March 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:		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;
	Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;		*Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;
	Is compact in file size;		*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 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.		*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.		SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Tanthony@uab.edu: created page with generic stub

2012-03-19T15:34:21Z

created page with generic stub

New page

{{Generic_stub}}

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:
<pre>
module load samtools/samtools
</pre>