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Everything licensed and supported by KAUST IT, in one place. Whether you're looking for a research or scientific application, a productivity tool, or a program used by your team or department, if IT supports it at KAUST, you'll find it here.

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SAM Tools

SAM Tools

SAM (Sequence Alignment / Map) Tools is a flexible generic format for storing nucleotide sequence alignment. SAM tools provide set of efficient utilities on manipulating alignments in the SAM format.
Support site:
http://www.htslib.org
Faculty/Researchers
Staff
Students

Linux installation instructions

Use modules to load the applications available in the scientific application stack. Please contact IT Linux Support or open a ticket with the IT Help Desk to install a new version of this application.

Loading SAMTools from the scientific application stack

$ module load samtools
Run SAMtools after loading the module
$ samtools <command> [options] 
SAM Tools manual pages
$ man samtools