SSAHA2

SSAHA2

SSAHA2

Overview

SSAHA2: Sequence Search and Alignment by Hashing Algorithm

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.

Download and Installation

Learn and Support

Detailed instructions can be found at

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

If you like SSAHA2 also check out the related software SMALT which is more accurate, efficient and simpler to use.

License and Citation

   Copyright (C) 2001 - 2015  Genome Research Ltd.                       

   Authors: Adam Spargo, Hannes Ponstingl and Zemin Ning                   
                                                                           
                                                                           
   SSAHA2 is free software: you can redistribute it and/or modify it       
   under the terms of the GNU General Public License as published by the   
   Free Software Foundation, either version 3 of the License, or (at your  
   option) any later version.                                              
                                                                           
   This program is distributed in the hope that it will be useful, but     
   WITHOUT ANY WARRANTY; without even the implied warranty of              
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU        
   General Public License for more details.                                
                                                                           
   You should have received a copy of the GNU General Public License along 
   with this program.  If not, see <http://www.gnu.org/licenses/>.

Contact

For more information, please contact:

Zemin Ning ( zn1@sanger.ac.uk ) or

Adam Spargo ( aws@sanger.ac.uk ) or

Hannes Ponstingl ( hp3@sanger.ac.uk )

 

Authors

Sanger Contributors

Publications

Tool Type