School of Life Sciences, Pharmacy and Chemistry, SEC Faculty, Kingston University, Kingston upon Thames, KT1 2EE, UK.
Sci Rep. 2017 Feb 22;7:43149. doi: 10.1038/srep43149.
This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are presented using a recently completed sequence of the genome of Lactobacillus fermentum 3872. In particular, quality of assemblies is assessed by using CLC Genomics Workbench read mapping and Optical mapping developed by OpGen. Over-extension of contigs without prior knowledge of contig location can lead to misassembled contigs, even when commonly used quality indicators such as read mapping suggest that a contig is well assembled. Precautions must also be undertaken when using long read sequencing technology, which may also lead to misassembled contigs.
本文对各种基因组测序方法进行了比较分析，重点是验证组装质量。使用最近完成的发酵乳杆菌 3872 基因组序列，展示了各种从头组装工具以及测序技术的比较评估结果。特别是，使用 CLC Genomics Workbench 读映射和 OpGen 开发的光学映射来评估组装的质量。在不知道 contig 位置的情况下过度扩展 contig 可能会导致组装错误的 contig，即使常用的质量指标（如读映射）表明 contig 组装良好。在使用长读测序技术时也必须采取预防措施，这也可能导致组装错误的 contig。
