De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.
De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.
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DOI：
10.1038/s41598-017-03996-z
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发表时间：
2017-06-21
影响因子：
4.6
通讯作者：
Ning Z
中科院分区：
文献类型：
--
作者：
Giordano F;Aigrain L;Quail MA;Coupland P;Bonfield JK;Davies RM;Tischler G;Jackson DK;Keane TM;Li J;Yue JX;Liti G;Durbin R;Ning Z
长读段测序技术如Pacific Biosciences和Oxford Nanopore MinION能够产生平均片段长度超过10，000个碱基对且最大长度达到100，000个碱基对的长测序读段。与短读段相比，从长读段测序平台获得的组装体具有高得多的重叠群连续性和基因组完整性，因为长片段能够将路径延伸到有问题的或重复的区域中。据报道，太平洋生物科学公司的技术有许多成功的组装应用，从小型细菌基因组到大型植物和动物基因组。最近，由于这种新型测序仪器的便携性和低成本，使用Oxford Nanopore MinION数据的基因组组装引起了人们的广泛关注。在本文中，我们使用三个不同的平台：MinION，PacBio和MiSeq对一个特征良好的基因组，酿酒酵母S288C菌株进行了重新测序。我们提出了一个全面的度量比较各种管道生成的组件，并讨论了平台相关的数据特性如何影响装配质量。在给定的31X读取深度下，来自Pacific Biosciences和Oxford Nanopore MinION的组装体对于16个核染色体显示出优异的连续性和完整性，但对于线粒体基因组则没有，其重建仍然是一个重大挑战。
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes. Recently, genome assemblies using Oxford Nanopore MinION data have attracted much attention due to the portability and low cost of this novel sequencing instrument. In this paper, we re-sequenced a well characterized genome, the Saccharomyces cerevisiae S288C strain using three different platforms: MinION, PacBio and MiSeq. We present a comprehensive metric comparison of assemblies generated by various pipelines and discuss how the platform associated data characteristics affect the assembly quality. With a given read depth of 31X, the assemblies from both Pacific Biosciences and Oxford Nanopore MinION show excellent continuity and completeness for the 16 nuclear chromosomes, but not for the mitochondrial genome, whose reconstruction still represents a significant challenge.