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Bioinformatics Advance Access originally published online on January 28, 2008
Bioinformatics 2008 24(5):713-714; doi:10.1093/bioinformatics/btn025
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SOAP: short oligonucleotide alignment program

Ruiqiang Li 1,2, Yingrui Li 1, Karsten Kristiansen 2 and Jun Wang 1,2,*

1Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark

*To whom correspondence should be addressed.


  Abstract

Summary: We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets.

Availability: http://soap.genomics.org.cn

Contact: soap{at}genomics.org.cn

Associate Editor: Keith Crandall

Received on November 10, 2007; revised on December 20, 2007; accepted on January 14, 2008

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