ena-STUDY-UC SANTA CRUZ-27-01-2015-06:50:44:491-796
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.
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.