SAMtools

SAM format is a generic format for storing large nucleotide sequence alignments. SAMtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Availability and Restrictions

The following versions of SAMtools are available on OSC clusters:

Version Oakley Owens pitzer
0.1.18 X    
1.3.1  X*  X*  
1.6 X X  
1.8     X*
1.9   X  
* Current default version

You can use  module spider samtools  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

SAMtools is available to all OSC users without restriction.

Publisher/Vendor/Repository and License Type

Genome Research Ltd., Open source

Usage on Oakley

Set-up

To configure your environment for use of SAMtools, run the following command:   module load samtools . The default version will be loaded. To select a particular SAMtools version, use   module load samtools/version . For example, use  module load samtools/1.3.1  to load SAMtools 1.3.1.

Usage on Owens

Set-up

To configure your environment for use of SAMtools, run the following command:    module load samtools  . The default version will be loaded. To select a particular SAMtools version, use    module load samtools/version  . For example, use   module load samtools/1.3.1   to load SAMtools 1.3.1.

Usage on Pitzer

Set-up

To configure your environment for use of SAMtools, run the following command:    module load samtools  . The default version will be loaded. 

Further Reading

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