Ragout-a reference-assisted assembly tool for bacterial genomes.
Ragout-a reference-assisted assembly tool for bacterial genomes.
复制标题
DOI：
10.1093/bioinformatics/btu280
复制
发表时间：
2014-06-15
期刊：
影响因子：
--
通讯作者：
Pham S
中科院分区：
文献类型：
--
作者：
Kolmogorov M;Raney B;Paten B;Pham S
摘要：细菌基因组比哺乳动物基因组简单，但从目前由高通量短读测序机产生的数据组装细菌基因组仍然会产生数百个重叠群。为了提高组装质量，最近的研究利用了更长的太平洋生物科学(PacBio)阅读或跳跃文库来将重叠群连接到更大的支架上，或者帮助组装者解决基因组重复区域中的歧义。然而，它们在当代基因组研究中的受欢迎程度仍然受到高成本和错误率的限制。在这项工作中，我们探索了通过使用密切相关物种/菌株的完整基因组来改进组装的可能性。我们提出了Ragout，一种基因组重排方法，来解决这个问题。与大多数只使用一个参考基因组的参考制导算法不同，Ragout使用多个参考以及这些参考之间的进化关系来确定重叠群的正确顺序。此外，Ragout使用装配图和多尺度同步块来减少由输入装配的小重叠群引起的装配间隙。在模拟和真实的数据集中，我们认为，对于常见的细菌物种，其中许多相关菌株的完整基因组序列已经可用，目前的高通量短读测序范例足以为每个染色体获得一个高质量的支架。上市时间：RAGOUT软件可在以下网站免费获得：https://github.com/fenderglass/Ragout.联系方式：spham@salk.edu
Summary: Bacterial genomes are simpler than mammalian ones, and yet assembling the former from the data currently generated by high-throughput short-read sequencing machines still results in hundreds of contigs. To improve assembly quality, recent studies have utilized longer Pacific Biosciences (PacBio) reads or jumping libraries to connect contigs into larger scaffolds or help assemblers resolve ambiguities in repetitive regions of the genome. However, their popularity in contemporary genomic research is still limited by high cost and error rates. In this work, we explore the possibility of improving assemblies by using complete genomes from closely related species/strains. We present Ragout, a genome rearrangement approach, to address this problem. In contrast with most reference-guided algorithms, where only one reference genome is used, Ragout uses multiple references along with the evolutionary relationship among these references in order to determine the correct order of the contigs. Additionally, Ragout uses the assembly graph and multi-scale synteny blocks to reduce assembly gaps caused by small contigs from the input assembly. In simulations as well as real datasets, we believe that for common bacterial species, where many complete genome sequences from related strains have been available, the current high-throughput short-read sequencing paradigm is sufficient to obtain a single high-quality scaffold for each chromosome. Availability: The Ragout software is freely available at: https://github.com/fenderglass/Ragout. Contact: spham@salk.edu
登录
查看更多内容
影响因子：
5.8
作者：
Richter, Daniel C.;Schuster, Stephan C.;Huson, Daniel H.
通讯作者：
Huson, Daniel H.
影响因子：
7
作者：
Paten, Benedict;Earl, Dent;Haussler, David
通讯作者：
Haussler, David
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
7
作者：
Ma, Jian;Zhang, Louxin;Miller, Webb
通讯作者：
Miller, Webb
影响因子：
7
作者：
Alekseyev, Max A.;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.