Archive Page: ssahaSNP

Archive Page: ssahaSNP


Archive Page - this page is maintained as a historical archive and is no longer being updated.


ssahaSNP: Sequence Search and Alignment by Hashing Algorithm

ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence.

Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. For those less repetitive or non-repetitive reads, we place them uniquely on the reference genome sequence and find the best alignment according to the pair-wise alignment score if there are multiple seeded regions. From the best alignment, SNP candidates are screened, taking into account the quality value of the bases with variation as well as the quality values in the neighbouring bases, using neighbourhood quality standard (NQS). For insertions/deletions, we check if the same indel is mapped by more than one read, ensuring the detected indel with high confidence.

Learn and Support

Contact the authors for more information.

License and Citation

Copyright (C) 2004 - 2010 Genome Research Ltd.

Authors: Zemin Ning, Adam Spargo and James Mullikin

SSAHA 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 <>.


Contact Zemin Ning or Adam Spargo for further information.


Sanger Contributors
External Contributors


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