A reference dataset for phage M13 dsDNA generated with the Oxford Nanopore MinION

Nanopore DNA strand sequencing was conceived in 1989. Proof of concept experiments over the ensuing decades set the stage for commercial development of a commercial device. In 2014, Oxford Nanopore Technologies released their ninety-gram MinION nanopore sequencer for beta-testing. Phage M13 is a widely used sequencing standard. We present a dataset for phage M13 double-stranded DNA sequenced on the MinION as part of the MinION Access Program (MAP). Three replicate sequencing experiments were run using the R7.3 chemistry (released in September 2014), and a total of over a gigabase of total sequence reported. In contrast to results using earlier chemistries we found that the vast majority high-quality 2D reads could be aligned back to reference, that they had 83% average percent identity using the LAST mapper and that many spanned the complete M13 genome. We provide the sequence data for dsDNA M13 experiments on the MinION in FASTQ format. These files should help development of informatics tools tailored for MinION data for genomics applications, in particular methods involving sequence alignment and base-level variant detection, as the short-nature of the genome and very deep sequencing allow a comprehensive evaluation of the base-level characteristics of the reads. In addition, base-called FAST5 files, in HDF5 format, are provided to help understand the structure and quality of the data. These should help the community in developing bioinformatics tools tailored for nanopore sequencing.

纳米孔DNA链测序技术的构想诞生于1989年。后续数十年间的概念验证实验，为该技术商用测序设备的开发奠定了坚实基础。2014年，牛津纳米孔科技公司（Oxford Nanopore Technologies）推出了重量仅90克的MinION纳米孔测序仪，启动公测。M13噬菌体是测序领域广泛使用的标准参照样本。本数据集包含通过MinION准入计划（MinION Access Program, MAP）完成的M13双链DNA测序数据。实验采用2014年9月发布的R7.3测序化学试剂，开展了三次重复测序实验，最终产出总序列量超过1吉碱基对。与早期测序化学试剂的结果相比，我们发现绝大多数高质量双向测序读段（2D reads）均可比对至参考基因组；经LAST比对工具（LAST mapper）分析后，其平均序列一致性可达83%，且多数读段可完整覆盖M13噬菌体基因组。我们以FASTQ格式提供了MinION平台上M13双链DNA（dsDNA）测序实验的序列数据。这批数据可助力适配MinION测序数据的基因组学生物信息学工具开发，尤其是针对序列比对与碱基级变异检测的相关方法——得益于该基因组长度较短且测序深度充足，可全面评估读段的碱基级特征。此外，我们还提供了经碱基识别的HDF5格式FAST5文件，以帮助研究者理解数据的结构与质量，这将助力纳米孔测序领域的生物信息学工具开发。