# ssaha2

## Summary

+ **Module Name:** ssaha2
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://www.sanger.ac.uk/resources/software/ssaha2/](http://www.sanger.ac.uk/resources/software/ssaha2/)

## Software Description

SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a
pairwise sequence alignment program designed for the efficient mapping
of sequencing reads onto genomic reference sequences.SSAHA2 reads of
most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a
range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up
pipeline for analysis and genotype calling is available as a separate
package.
## General Linux

To load this module for use in a Linux environment, you can run the command:

	module load ssaha2

Depending on where you are working, there may be more than one version of ssaha2 available.
To see which modules are available for loading you can run:

	module avail ssaha2