De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads
De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads
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DOI：
10.1093/bioinformatics/btt590
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发表时间：
2014-01-01
期刊：
影响因子：
5.8
通讯作者：
Schrenzel, Jacques
中科院分区：
文献类型：
--
作者：
Hernandez, David;Tewhey, Ryan;Schrenzel, Jacques
动机：成对末端测序可以绕过第二代测序仪产生的短阅读，对于基因组的从头组装是必不可少的。然而，从短阅读中获得完整的基因组仍然是一个开放的挑战。我们提出了一种算法，该算法利用潜在任意长度的插入所发出的配对信息。该方法使用约束搜索树来确定通过重叠图的路径。我们还提出了一种方法，该方法根据上下文覆盖自动确定合适的重叠界限，从而减少了手动参数化的需要。结果：我们通过组装两株在Illumina平台上测序的金黄色葡萄球菌对我们的方法进行了评估。使用100个碱基对的末端阅读和最小的人工筛选，我们产生了之前未描述的分离株SGH-10-168的完整基因组序列。
Motivation: Paired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions.Results: We assess our methods by assembling two Staphylococcus aureus strains that were sequenced on the Illumina platform. Using 100 bp paired-end reads and minimal manual curation, we produce a finished genome sequence for the previously undescribed isolate SGH-10-168.