The phusion assembler
The phusion assembler
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DOI：
10.1101/gr.731003
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发表时间：
2003-01-01
期刊：
影响因子：
7
通讯作者：
Ning, ZM
中科院分区：
文献类型：
--
作者：
Mullikin, JC;Ning, ZM
Phusion组装器利用小鼠基因组测序联盟收集的全基因组鸟枪法（WGS）数据集，在约7.5倍的序列覆盖度下组装了小鼠基因组，产生了一个大小为26亿碱基对的高质量草图组装结果，其中90%的碱基位于479个支架中。对于小鼠这种庞大且富含重复序列的基因组，输入数据集经过设计，包含了高比例的各种大小选定插入片段（长度从2 - 200千碱基对不等）的配对末端序列，并插入到各种宿主载体模板中。Phusion利用序列数据（称为读段）以及关于共享共同模板的读段的信息（称为读段对），将这个大基因组组装成高度准确的结果。预组装阶段将读段聚类为合理的组，这是整个组装器的一个关键要素，因为它允许对组装阶段采用一种简单的并行化方法，因为每个聚类都可以独立于其他聚类进行处理。除了将Phusion应用于小鼠基因组外，我们还将展示秀丽隐杆线虫全基因组鸟枪法组装的结果，其测序覆盖度约为11倍。秀丽隐杆线虫的组装结果已通过欧洲分子生物学实验室（EMBL）存档，网址为http://www.ebi.ac.uk/services/index.html，使用系列编号CAAC01000001 - CAAC01000578，然而此处描述的Phusion小鼠组装结果未存档。小鼠数据由小鼠基因组测序联盟生成。秀丽隐杆线虫的序列由维康桑格研究所和华盛顿大学医学院基因组测序中心生成。
The Phusion assembler has assembled the mouse genome from the whole-genome shotgun (WGS) dataset collected by the Mouse Genome Sequencing Consortium, at -7.5x sequence coverage, producing a high-quality draft assembly 2.6 gigabases in size, of which 90% of these bases are in 479 scaffolds. For the mouse genome, which is a large and repeat-rich genome, the input dataset was designed to include a high proportion of paired end sequences of various size selected inserts, from 2-200 kbp lengths, into various host vector templates. Phusion uses sequence data, called reads, and information about reads that share common templates, called read pairs, to drive the assembly of tills large genome to highly accurate results. The preassembly stage, which clusters the reads into sensible groups, is a key element of the entire assembler, because it permits a simple approach to parallelization of the assembly stage, as each cluster can be treated independent of the others. In addition to the application of Phusion to the mouse genome, we will also present results from the WGS assembly of Caenorhabditis briggsae sequenced to about 11x coverage. The C. briggsae assembly was accessioned through EMBL, http://www.ebi.ac.uk/services/index.html, using the series CAAC01000001-CAAC01000578, however, the Phusion mouse assembly described here was not accessioned. The mouse data was generated by the Mouse Genome Sequencing Consortium. The C. briggsae sequence was generated at The Wellcome Trust Sanger Institute and the Genome Sequencing Center, Washington University School of Medicine.