Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens
Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens
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DOI：
10.1038/srep28625
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发表时间：
2016-06-28
影响因子：
4.6
通讯作者：
May, Gregory
中科院分区：
文献类型：
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作者：
Deschamps, Stephane;Mudge, Joann;May, Gregory
MinION是一种便携式单分子DNA测序仪，由Oxford Nanopore Technologies于2014年发布，通过测量单链DNA分子通过孔移位时离子流的变化来产生长测序读数。虽然MinION长读段的错误率远高于短读段测序技术产生的错误率，但它们可以在初始校正步骤后生成微生物基因组的从头组装，该初始校正步骤包括Illumina测序数据的比对或Oxford Nanopore读段之间的重叠检测以提高准确性。在这项研究中，MinION读取从根癌农杆菌菌株LBA4404的多染色体基因组产生。首先通过与内部参考组件比较来表征共有双向（有义和反义）“2D”序列中的错误。进行基于Illumina的校正和自校正，并且将所得的校正读数组装成高质量的杂交和非杂交组装体。随后比较了校正的读取数据集和组件。这里显示的结果表明，杂交和非杂交方法都可以用于将Oxford Nanopore读数组装成信息丰富的多染色体组装体，每个组装体在邻接性和准确性方面具有略微不同的结果。
The MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded DNA molecules translocate through the pores. While MinION long reads have an error rate substantially higher than the ones produced by short-read sequencing technologies, they can generate de novo assemblies of microbial genomes, after an initial correction step that includes alignment of Illumina sequencing data or detection of overlaps between Oxford Nanopore reads to improve accuracy. In this study, MinION reads were generated from the multi-chromosome genome of Agrobacterium tumefaciens strain LBA4404. Errors in the consensus two-directional (sense and antisense) "2D" sequences were first characterized by way of comparison with an internal reference assembly. Both Illumina-based correction and self-correction were performed and the resulting corrected reads assembled into high-quality hybrid and non-hybrid assemblies. Corrected read datasets and assemblies were subsequently compared. The results shown here indicate that both hybrid and non-hybrid methods can be used to assemble Oxford Nanopore reads into informative multi-chromosome assemblies, each with slightly different outcomes in terms of contiguity and accuracy.