Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology
Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology
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DOI：
10.1099/mgen.0.000085
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发表时间：
2016-09-01
影响因子：
3.9
通讯作者：
Peacock, Sharon J.
中科院分区：
文献类型：
--
作者：
Judge, Kim;Hunt, Martin;Peacock, Sharon J.
将Oxford Nanopore MinION测序技术转化为医学微生物学需要持续的分析，以跟上仪器的技术改进和相关分析软件的发布。在这里，我们使用耐多药神户肠杆菌分离株作为模式生物，比较用于组装基因组数据的开源软件，并将其与生成可操作信息所需的时间相关联。三种软件工具（PBcR、Canu和miniasm）用于组装MinION数据，第四种（SPAdes）用于联合收割机MinION和Illumina数据以产生混合组装。所有四个具有相似数量的重叠群，并且比单独使用Illumina数据的组装更连续，其中SPAdes产生单个染色体重叠群。评估四个组装体以代表基因组结构，揭示了SPAdes组装体中的单个大倒位，其也不正确地将质粒整合到染色体重叠群中。在前6、9和12小时分别生成了几乎50%、80%和90%的MinION通过读数。单独使用前6小时的数据导致不太准确的片段化组装，但前9或12小时的数据产生与48小时测序相似的组装。使用Canu在2小时内生成组装体，这表明在不到48小时的时间内可以从分离株到组装数据。MinION数据确定，负责耐药的基因分别由编码碳青霉烯类和磺胺类、利福平和氨基糖苷类耐药的两种质粒携带。
Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software. Here, we use a multidrug-resistant Enterobacter kobei isolate as a model organism to compare open source software for the assembly of genome data, and relate this to the time taken to generate actionable information. Three software tools (PBcR, Canu and miniasm) were used to assemble MinION data and a fourth (SPAdes) was used to combine MinION and Illumina data to produce a hybrid assembly. All four had a similar number of contigs and were more contiguous than the assembly using Illumina data alone, with SPAdes producing a single chromosomal contig. Evaluation of the four assemblies to represent the genome structure revealed a single large inversion in the SPAdes assembly, which also incorrectly integrated a plasmid into the chromosomal contig. Almost 50 %, 80 % and 90 % of MinION pass reads were generated in the first 6, 9 and 12 h, respectively. Using data from the first 6 h alone led to a less accurate, fragmented assembly, but data from the first 9 or 12 h generated similar assemblies to that from 48 h sequencing. Assemblies were generated in 2 h using Canu, indicating that going from isolate to assembled data is possible in less than 48 h. MinION data identified that genes responsible for resistance were carried by two plasmids encoding resistance to carbapenem and to sulphonamides, rifampicin and aminoglycosides, respectively.