Skip Navigation


Bioinformatics Advance Access originally published online on June 3, 2009
Bioinformatics 2009 25(15):1966-1967; doi:10.1093/bioinformatics/btp336
This Article
Right arrow Full Text
Right arrow Full Text (Print PDF)
Right arrow All Versions of this Article:
25/15/1966    most recent
btp336v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Li, R.
Right arrow Articles by Wang, J.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, R.
Right arrow Articles by Wang, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SOAP2: an improved ultrafast tool for short read alignment

Ruiqiang Li 1,2,{dagger}, Chang Yu 1,{dagger}, Yingrui Li 1, Tak-Wah Lam 3, Siu-Ming Yiu 3, Karsten Kristiansen 2 and Jun Wang 1,2,*

1 Beijing Genomics Institute at Shenzhen, Shenzhen, 518083, China, 2 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark and 3 Department of Computer Science, University of Hong Kong, Hong Kong, China

* To whom correspondence should be addressed.


  Abstract

Summary: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20–30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome.

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

Contact: soap{at}genomics.org.cn

{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: Joaquin Dopazo

Received on January 23, 2009; revised on April 27, 2009; accepted on May 24, 2009

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
D. S. Horner, G. Pavesi, T. Castrignano, P. D. De Meo, S. Liuni, M. Sammeth, E. Picardi, and G. Pesole
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
Brief Bioinform, October 27, 2009; (2009) bbp046v1.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.