Short read fragment assembly of bacterial genomes

被引:276
作者
Chaisson, Mark J. [2 ]
Pevzner, Pavel A. [1 ]
机构
[1] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA
[2] Univ Calif San Diego, Bioinformat Program, La Jolla, CA 92093 USA
关键词
D O I
10.1101/gr.7088808
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
In the last year, high-throughput sequencing technologies have progressed from proof-of-concept to production quality. While these methods produce high-quality reads, they have yet to produce reads comparable in length to Sanger-based sequencing. Current fragment assembly algorithms have been implemented and optimized for mate-paired Sanger-based reads, and thus do not perform well on short reads produced by short read technologies. We present a new Eulerian assembler that generates nearly optimal short read assemblies of bacterial genomes and describe an approach to assemble reads in the case of the popular hybrid protocol when short and long Sanger-based reads are combined.
引用
收藏
页码:324 / 330
页数:7
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