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Bioinformatics Advance Access originally published online on August 6, 2008
Bioinformatics 2008 24(21):2431-2437; doi:10.1093/bioinformatics/btn416
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ZOOM! Zillions of oligos mapped

Hao Lin 1,{dagger}, Zefeng Zhang 1,{dagger}, Michael Q. Zhang 2, Bin Ma 3,* and Ming Li 4,*

1Institute for Computing Technology, Chinese Academy of Sciences, Beijing, China, 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, 3Department of Computer Science, University of Western Ontario, London, ON. N6A 5B8, Canada and 4David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON. N2L 3G1, Canada

*To whom correspondence should be addressed.


  Abstract

Motivation: The next generation sequencing technologies are generating billions of short reads daily. Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare transcripts.

Results: We present a framework for how full sensitivity mapping can be done in the most efficient way, via spaced seeds. Using the framework, we have developed software called ZOOM, which is able to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.

Availability: ZOOM is freely available to non-commercial users at http://www.bioinfor.com/zoom

Contact: bma{at}csd.uwo.ca, mli{at}uwaterloo.ca

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Limsoon Wong

Received on June 23, 2008; revised on July 31, 2008; accepted on August 1, 2008

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