ARACHNE: A whole-genome shotgun assembler
ARACHNE: A whole-genome shotgun assembler
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DOI：
10.1101/gr.208902
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发表时间：
2002-01-01
期刊：
影响因子：
7
通讯作者：
Lander, ES
中科院分区：
文献类型：
--
作者：
Batzoglou, S;Jaffe, DB;Lander, ES
我们描述了一种新的计算机系统，称为ARACHNE，用于使用成对端全基因组霰弹枪读取来组装基因组序列。ARACHNE具有几个关键功能，包括高效灵敏的查找读取重叠的程序，通过在组装前纠正错误实现高精度的重叠评分程序，基于正反向链接的读取合并，以及通过正反向链接不一致性检测重复配置。为了测试ARACHNE，我们创建了模拟读取，为流感嗜血杆菌、酿酒葡萄球菌和黑葡萄球菌以及人类第21和22号染色体的基因组提供了接近10倍的覆盖范围。这些模拟reads的组装几乎完全覆盖了各自的基因组，少量的contigs连接到少量的超contigs（或支架）中。例如，对A melanogaster基因组的分析获得了接近98%的覆盖率，N50 contig长度为324 kb， N50超contig长度为5143 kb。装配精度很高，尽管不是完美的：每1mb大约发生1个小错误（通常是大小接近1kb的删除），其他错误装配的数量非常少。组装速度很快：果蝇组装只需要在一个667mhz的处理器上运行21个小时，使用8.4 Gb的内存。
We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy by correcting errors before assembly, read merger based on forward-reverse links, and detection of repeat contigs by forward-reverse link inconsistency. To test ARACHNE, we created simulated reads providing similar to10-fold coverage of the genomes of H. influenzae, S. cerevisiae, and A melanogaster, as well as human chromosomes 21 and 22. The assemblies of these simulated reads yielded nearly complete coverage of the respective genomes, with a small number of contigs joined into a smaller number of supercontigs (or scaffolds). For example, analysis of the A melanogaster genome yielded similar to98% coverage with an N50 contig length of 324 kb and an N50 supercontig length of 5143 kb. The assembly accuracy was high, although not perfect: small errors occurred at a frequency of roughly 1 per 1 Mb (typically, deletion of similar to1 kb in size), with a very small number of other misassemblies. The assembly was rapid: the Drosophila assembly required only 21 hours on a single 667 MHz processor and used 8.4 Gb of memory.