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Bioinformatics Advance Access published online on April 15, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp255
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MapView: visualization of short reads alignment on a desktop computer

Hua Bao 1,§,*, Hui Guo 1,§, Jinwei Wang 2, Renchao Zhou 1, Xuemei Lu 1 and Suhua Shi 1

1State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of Ministry of Education, School of Life Sci-ences, Sun Yat-Sen University, Guangzhou, 510275, China
2School of Manufacturing Science and Engineering, Sichuan University, Chengdu, 610064, China

*To whom correspondence should be addressed. Dr. Hua Bao, E-mail: baohua100{at}hotmail.com


  Abstract

Summary: We introduce a new visual analytics tool named MapView to facilitate the representation of large-scale short reads alignment data and genetic variation analysis. MapView can handle hundreds of millions of short reads on a desktop computer with limited memory. It supports a compact alignment view for both single-end and paired-end short reads, multiple navigation and zoom modes, and multi-thread processing. Moreover, MapView offers automated genetic variation detection. MapView has been used in our lab and by over 10 research labs worldwide.

Availability: http://evolution.sysu.edu.cn/mapview/.

Contact: baohua100@hotmail.com

Supplementary information: http://evolution.sysu.edu.cn/mapview/MVF.pdf

Associate Editor: Dr. Joaquin Dopazo

§These authors contributed equally to this work.

Received on March 10, 2009; revised on April 8, 2009; accepted on April 8, 2009

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