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Bioinformatics Advance Access published online on August 6, 2008
Bioinformatics, 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 a,*, Zefeng Zhang a,*, Michael Q. Zhang b, Bin Ma c,{dagger} and Ming Li d,{dagger}

aInstitute of Computing Technology, Chinese Academy of Sciences
bCold Spring Harbor Laboratory
cDepartment of Computer Science, University of Western Ontario
dDavid R. Cheriton School of Computer Science, University of Waterloo

{dagger}To whom correspondence should be addressed. Bin Ma, E-mail: bma{at}csd.uwo.ca


  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: hlin{at}bioinfor.com, zzhang{at}bioinfor.com, bma{at}csd.uwo.ca

Associate Editor: Dr. Limsoon Wong

* These authors contributed equally to this work.

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

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