ssahaSNP is a tool for the detection of SNPs and short indels using the first generation capillary sequencing reads.

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.


The package can be downloaded from

Further information

Copyright (C) 2008 – 2015 Genome Research Ltd.

Author: Zemin Ning

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If you need help or have any queries, please contact us using the details below.

For more information, please contact:

Zemin Ning ( )

Sanger Institute Contributors

Photo of Dr Zemin Ning

Dr Zemin Ning

Senior Scientific Manager