ssahaSNP

ssahaSNP

ssahaSNP

Overview

Fast and accurate detection of genomic polymorphism is increasingly under demand, fuelled by many large genome projects. The software package ssahaSNP detects homozygous SNPs and insertion/deletion events on a eukaryotic genome scale from millions of shotgun reads. Matching seeds of a few kmer words are found to locate the position of the read on the genome. Full sequence alignment is then performed to detect base variations. Quality values of both variation bases and neighbouring bases are checked to exclude possible sequence base errors. To increase the accuracy of detection in some cases, it requires that the same mutation event is mapped by two or more shotgun reads.

Download and Installation

License and Citation

Copyright (C) 2008 - 2015 Genome Research Ltd.

Author: Zemin Ning


Phusion2 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 )

Authors

Sanger Contributors

Publications

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