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
The package can be downloaded from
Learn and Support
Detailed instructions can be found at
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/>.
For more information, please contact:
Zemin Ning ( firstname.lastname@example.org ) or
Adam Spargo ( email@example.com ) or
Hannes Ponstingl ( firstname.lastname@example.org )
SSAHA: a fast search method for large DNA databases.
Genome research 2001;11;10;1725-9
ssahaSNP - a polymorphism detection tool on a whole genome scale
Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE 2005;251 - 252
The SSAHA trace server
Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE 2004;544 - 545