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A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer
Joshua Quick1, Aaron R Quinlan2, Nicholas J Loman3
1Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK ; NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham B15 2TT, UK.
Gigascience
|November 12, 2014
Summary
The MinION™ is a portable DNA sequencer. This study presents sequencing data from Escherichia coli K-12, generated using MinION™ R7 and R7.3 chemistries, to aid in developing new bioinformatics tools.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The MinION™ is a portable, USB-powered single-molecule sequencer by Oxford Nanopore Technologies.
- It sequences DNA by measuring current changes as strands pass through a protein nanopore.
- This technology enables real-time nucleotide sequence determination.
Purpose of the Study:
- To present a dataset from whole-genome shotgun sequencing of Escherichia coli K-12.
- To showcase data generated by the MinION™ during its early access program.
- To encourage development of novel bioinformatics methods for nanopore sequencing data.
Main Methods:
- Whole-genome shotgun sequencing of Escherichia coli K-12 substr. MG1655.
- Data generation using the MinION™ device with R7 (July 2014) and R7.3 (September 2014) chemistries.
- Provision of base-called sequence data and FAST5 event data.
Main Results:
- A read dataset from Escherichia coli K-12 whole-genome sequencing is presented.
- Sequencing performance using two distinct MinION™ chemistries (R7 and R7.3) is demonstrated.
- The study provides raw and processed data for further analysis.
Conclusions:
- The provided data illustrate the output of the MinION™ sequencing platform.
- Encourages the development of custom bioinformatics tools for alignment, assembly, and variant calling.
- Facilitates improvement of base-calling algorithms using event data.
