a computer simulator for assessing different challenges and strategies of de novo sequence assembly电脑模拟器评估新创序列组装不同的挑战和策略.pdfVIP

Genes 2010, 1, 263-282; doi:10.3390/genes1020263 OPEN ACCESS genes ISSN 2073-4425 /journal/genes Article A Computer Simulator for Assessing Different Challenges and Strategies of de Novo Sequence Assembly Bjarne Knudsen 1, Roald Forsberg 1 and Michael M. Miyamoto 2,* 1 CLC bio, 8200 Aarhus N, Denmark; E-Mails: bknudsen@ (B.K.); rforsberg@ (R.F.) 2 Department of Biology, Box 118525, University of Florida, Gainesville, Florida, 32611-8525, USA * Author to whom correspondence should be addressed; E-Mail: miyamoto@; Tel.: +1 352-392-3275; Fax: +1 352-392-3704. Received: 1 June 2010; in revised form: 18 August 2010 / Accepted: 31 August 2010 / Published: 13 September 2010 Abstract: This study presents a new computer program for assessing the effects of different factors and sequencing strategies on de novo sequence assembly. The program uses reads from actual sequencing studies or from simulations with a reference genome that may also be real or simulated. The simulated reads can be created with our read simulator. They can be of differing length and coverage, consist of paired reads with varying distance, and include sequencing errors such as color space miscalls to imitate SOLiD data. The simulated or real reads are mapped to their reference genome and our assembly simulator is then used to obtain optimal assemblies that are limited only by the