Short read fragment assembly of bacterial genomes
Short read fragment assembly of bacterial genomes
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DOI：
10.1101/gr.7088808
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发表时间：
2008-02-01
期刊：
影响因子：
7
通讯作者：
Pevzner, Pavel A.
中科院分区：
文献类型：
--
作者：
Chaisson, Mark J.;Pevzner, Pavel A.
去年，高通量测序技术从概念验证到生产质量发展。尽管这些方法产生了高质量的读取，但它们尚未产生与基于Sanger的测序相当的读取。当前的片段组装算法已经针对基于序列的sanger读数实施和优化，因此在短读技术产生的简短读取中表现不佳。我们提出了一个新的Eulerian汇编程序，该组件将生成细菌基因组的几乎最佳的简短读取组件，并描述在流行混合协议的情况下，将基于简短和长的基于Sanger的读取组合在一起时，在流行的混合协议中进行了组装读取方法。
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.