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Bioinformatics Advance Access published online on July 2, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp403
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SNP-o-matic

Heinrich Magnus Manske 1,* and Dominic P. Kwiatkowski 1

1Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK

*To whom correspondence should be addressed. Dr. Heinrich Magnus Manske, E-mail: mm6{at}sanger.ac.uk


  Abstract

Motivation: High throughput sequencing technologies generate large amounts of short reads. Mapping these to a reference sequence consumes large amounts of processing time and memory, and read mapping errors can lead to noisy or incorrect alignments. SNP-o-matic is a fast, memory-efficient, and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on geno-typing.

Availability: http://snpomatic.sourceforge.net

Contact: mm6{at}sanger.ac.uk

Associate Editor: Dr. Limsoon Wong

Received on March 27, 2009; revised on June 12, 2009; accepted on June 27, 2009

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