Skip Navigation



Bioinformatics Advance Access published online on January 28, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn025
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
24/5/713    most recent
btn025v1
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.
Right arrow Search for Related Content
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 (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.
2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark.

*To whom correspondence should be addressed. Dr. Ruiqiang Li, E-mail: lirq{at}genomics.org.cn


  Abstract

Motivation: 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 multithreaded 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: Prof. Keith Crandall

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

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
 Genome ResHome page
H. M. Manske and D. P. Kwiatkowski
LookSeq: A browser-based viewer for deep sequencing data
Genome Res., November 1, 2009; 19(11): 2125 - 2132.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. D. Smith, W.-Y. Chung, E. Hodges, J. Kendall, G. Hannon, J. Hicks, Z. Xuan, and M. Q. Zhang
Updates to the RMAP short-read mapping software
Bioinformatics, November 1, 2009; 25(21): 2841 - 2842.
[Abstract] [Full Text] [PDF]

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]

Home page
 ScienceHome page
Q. Xia, Y. Guo, Z. Zhang, D. Li, Z. Xuan, Z. Li, F. Dai, Y. Li, D. Cheng, R. Li, et al.
Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx)
Science, October 16, 2009; 326(5951): 433 - 436.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
D. Moldovan, A. Spriggs, J. Yang, B. J. Pogson, E. S. Dennis, and I. W. Wilson
Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis
J. Exp. Bot., October 8, 2009; (2009) erp296v1.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Chen, T. Souaiaia, and T. Chen
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
Bioinformatics, October 1, 2009; 25(19): 2514 - 2521.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. D. Gawronski, S. M. S. Wong, G. Giannoukos, D. V. Ward, and B. J. Akerley
Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung
PNAS, September 22, 2009; 106(38): 16422 - 16427.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. M. Manske and D. P. Kwiatkowski
SNP-o-matic
Bioinformatics, September 15, 2009; 25(18): 2434 - 2435.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Gaidatzis, K. Jacobeit, E. J. Oakeley, and M. B. Stadler
Overestimation of alternative splicing caused by variable probe characteristics in exon arrays
Nucleic Acids Res., September 1, 2009; 37(16): e107 - e107.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. Weese, A.-K. Emde, T. Rausch, A. Doring, and K. Reinert
RazerS--fast read mapping with sensitivity control
Genome Res., September 1, 2009; 19(9): 1646 - 1654.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
P. F. Stadler, J. J.-L. Chen, J. Hackermuller, S. Hoffmann, F. Horn, P. Khaitovich, A. K. Kretzschmar, A. Mosig, S. J. Prohaska, X. Qi, et al.
Evolution of Vault RNAs
Mol. Biol. Evol., September 1, 2009; 26(9): 1975 - 1991.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Li, C. Yu, Y. Li, T.-W. Lam, S.-M. Yiu, K. Kristiansen, and J. Wang
SOAP2: an improved ultrafast tool for short read alignment
Bioinformatics, August 1, 2009; 25(15): 1966 - 1967.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Li and R. Durbin
Fast and accurate short read alignment with Burrows-Wheeler transform
Bioinformatics, July 15, 2009; 25(14): 1754 - 1760.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
S. Kawaoka, N. Hayashi, Y. Suzuki, H. Abe, S. Sugano, Y. Tomari, T. Shimada, and S. Katsuma
The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes
RNA, July 1, 2009; 15(7): 1258 - 1264.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Bao, H. Guo, J. Wang, R. Zhou, X. Lu, and S. Shi
MapView: visualization of short reads alignment on a desktop computer
Bioinformatics, June 15, 2009; 25(12): 1554 - 1555.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
R. Li, Y. Li, X. Fang, H. Yang, J. Wang, K. Kristiansen, and J. Wang
SNP detection for massively parallel whole-genome resequencing
Genome Res., June 1, 2009; 19(6): 1124 - 1132.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Jung Kim, N. Teletia, V. Ruotti, C. A. Maher, A. M. Chinnaiyan, R. Stewart, J. A. Thomson, and J. M. Patel
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches
Bioinformatics, June 1, 2009; 25(11): 1424 - 1425.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. C. Schatz
CloudBurst: highly sensitive read mapping with MapReduce
Bioinformatics, June 1, 2009; 25(11): 1363 - 1369.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
K. D. Passalacqua, A. Varadarajan, B. D. Ondov, D. T. Okou, M. E. Zwick, and N. H. Bergman
Structure and Complexity of a Bacterial Transcriptome
J. Bacteriol., May 15, 2009; 191(10): 3203 - 3211.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
N. Fahlgren, C. M. Sullivan, K. D. Kasschau, E. J. Chapman, J. S. Cumbie, T. A. Montgomery, S. D. Gilbert, M. Dasenko, T. W.H. Backman, S. A. Givan, et al.
Computational and analytical framework for small RNA profiling by high-throughput sequencing
RNA, May 1, 2009; 15(5): 992 - 1002.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. A. Ebhardt, H. H. Tsang, D. C. Dai, Y. Liu, B. Bostan, and R. P. Fahlman
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
Nucleic Acids Res., May 1, 2009; 37(8): 2461 - 2470.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. J. Fullwood, C.-L. Wei, E. T. Liu, and Y. Ruan
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
Genome Res., April 1, 2009; 19(4): 521 - 532.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. Campagna, A. Albiero, A. Bilardi, E. Caniato, C. Forcato, S. Manavski, N. Vitulo, and G. Valle
PASS: a program to align short sequences
Bioinformatics, April 1, 2009; 25(7): 967 - 968.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. L. Eaves and Y. Gao
MOM: maximum oligonucleotide mapping
Bioinformatics, April 1, 2009; 25(7): 969 - 970.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
K. V. Voelkerding, S. A. Dames, and J. D. Durtschi
Next-Generation Sequencing: From Basic Research to Diagnostics
Clin. Chem., April 1, 2009; 55(4): 641 - 658.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
X. Wang, A. A. Elling, X. Li, N. Li, Z. Peng, G. He, H. Sun, Y. Qi, X. S. Liu, and X. W. Deng
Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize
PLANT CELL, April 1, 2009; 21(4): 1053 - 1069.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
J. A. Reinhardt, D. A. Baltrus, M. T. Nishimura, W. R. Jeck, C. D. Jones, and J. L. Dangl
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
Genome Res., February 1, 2009; 19(2): 294 - 305.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Li, L. Ma, C. Song, Z. Yang, X. Wang, H. Huang, Y. Li, R. Li, X. Zhang, H. Yang, et al.
The YH database: the first Asian diploid genome database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D1025 - D1028.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. Kapur, H. Jiang, Y. Xing, and W. H. Wong
Cross-hybridization modeling on Affymetrix exon arrays
Bioinformatics, December 15, 2008; 24(24): 2887 - 2893.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
B. D. Ondov, A. Varadarajan, K. D. Passalacqua, and N. H. Bergman
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
Bioinformatics, December 1, 2008; 24(23): 2776 - 2777.
[Abstract] [Full Text] [PDF]

Home page
 J. Mol. Diagn.Home page
J. R. ten Bosch and W. W. Grody
Keeping Up With the Next Generation: Massively Parallel Sequencing in Clinical Diagnostics
J. Mol. Diagn., November 1, 2008; 10(6): 484 - 492.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Jiang and W. H. Wong
SeqMap: mapping massive amount of oligonucleotides to the genome
Bioinformatics, October 15, 2008; 24(20): 2395 - 2396.
[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.