Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
复制标题
复杂细菌基因组混合组装中长读长测序技术的比较
DOI：
10.1101/530824
复制
发表时间：
2019
期刊：
影响因子：
--
通讯作者：
De Maio N
中科院分区：
文献类型：
--
作者：
De Maio N
Illumina测序允许快速、廉价和准确的全基因组细菌分析，但短读段（<300 bp）通常不能实现完整的基因组组装。长读测序极大地有助于解析复杂的细菌基因组，特别是当与短读Illumina数据（混合组装）相结合时。然而，尚不清楚不同的长读段测序方法如何影响杂交组装准确性。组装过程的相对自动化对于促进高通量完整细菌基因组重建，避免多个定制过滤和数据操作步骤也至关重要。在这项研究中，我们使用Illumina测序和来自Oxford Nanopore Technologies（ONT）或SMRT Pacific Biosciences（PacBio）测序平台的长读段比较了20种细菌分离株（包括两种参考菌株）的杂交组装。我们选择了来自肠杆菌科的分离株，因为这些分离株通常具有高度可塑性，重复的遗传结构，并且这些物种的完整基因组重建与精确了解抗菌素耐药性的流行病学有关。Wede使用混合汇编程序Unicycler对基因组进行了新的组装，并比较了不同的读取处理策略，以及与Flye的长只读组装以及Pilon的短读取抛光进行了比较。使用PacBio或ONT读取的混合组装促进了高质量的基因组重建，并且在准确性和完整性方面优于长读取组装和抛光方法。ONT和Illumina读数的结合完全解析了大多数基因组，无需额外的手动步骤，并且在我们的环境中每个分离株的消耗品成本较低。自动化杂交组装是一个强大的工具，完整和准确的细菌基因组组装。
Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the familyEnterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. Wede novoassembled genomes using the hybrid assembler Unicycler and compared different read processing strategies, as well as comparing to long-read-only assembly with Flye followed by short-read polishing with Pilon. Hybrid assembly with either PacBio or ONT reads facilitated high-quality genome reconstruction, and was superior to the long-read assembly and polishing approach evaluated with respect to accuracy and completeness. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly.
登录
查看更多内容
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
3.7
作者：
Walker BJ;Abeel T;Shea T;Priest M;Abouelliel A;Sakthikumar S;Cuomo CA;Zeng Q;Wortman J;Young SK;Earl AM
通讯作者：
Earl AM
影响因子：
46.9
作者：
Kolmogorov, Mikhail;Yuan, Jeffrey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
肠沙门氏菌鼠伤寒菌株 Demerec 保藏培养物中噬菌体类型的多样性
影响因子：
4.4
作者：
W. Rabsch;R. Allen Helm;A. Eisenstark
通讯作者：
A. Eisenstark