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SSAHA2 on Helix

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. It was developed at the Wellcome Trust Sanger Institute, UK.

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.

The available version(s) of SSAHA2 can be seen by typing 'module avail ssaha2'. The SSAHA2 and Pileup executables need to be added to your path before running Ssaha2. This is most easily done by using the modules commands, as in the example below.

The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.

[user@helix]$ module avail ssaha2
----------------------------------- /usr/local/Modules/3.2.9/modulefiles -----------------------------------
ssaha2/2.5.3

[user@helix]$ module load ssaha2

[user@helix]$ module list
Currently Loaded Modulefiles:
  1) ssaha2/2.5.3

[user@helix]$ module unload ssaha2

[user@helix]$ module load ssaha2/2.5.3
[user@helix]$ module list
Currently Loaded Modulefiles:
  1) ssaha2/2.5.3

[user@helix]$ module show ssaha2
-------------------------------------------------------------------
/usr/local/Modules/3.2.9/modulefiles/ssaha2/2.5.3:

module-whatis    Sets up SSAHA2 2.5.3 
prepend-path     PATH /usr/local/apps/ssaha2/2.5.3 
prepend-path     PATH /usr/local/pileup 
-------------------------------------------------------------------

How To Use

If you have multiple runs (such as 4 runs) or longer runs (such as > 1 hours), apply for a Biowulf account (which comes free with helix account) and run your jobs on Biowulf cluster. See SSAHA2 on biowulf.

Example - Map 454 reads against the human genome

Load the ssaha2 module so that the executables are in your path.

module load ssaha2

Create a directory for this run.

$ mkdir /data/user/ssaha2/run1;cd /data/user/ssaha2/run1

Generate the hash index

$ ssaha2Build -454 -save htab NCBI36.fa

This command generates the hash table files hs36htab.base, hs36htab.body, hs36htab.head, hs36htab.name, hs36htab.size.

Single Reads - Assuming the reads are in the FASTQ file hs454.fq run the mapper with

ssaha2 -454 -output sam -outfile mapped.sam -save htab hs454.fq

This will write mappings to the files mapped.sam in SAM format.

Paired-end Reads - Assuming the mates of the read pairs are in the FASTQ files hs454 1.fq and hs454 2.fq. Run the mapper with the options

ssaha2 -454 -pair 200,3000 -output sam -outfile mapped.sam -save htab hs454_1.fq hs454_2.fq

This will write mapped and unmapped reads to the files mapped.sam in SAM format.

Documentation

ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf