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. 2014 Oct 20:3:22.
doi: 10.1186/2047-217X-3-22. eCollection 2014.

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

Joshua Quick  1 , Aaron R Quinlan  2 , Nicholas J Loman  3
Affiliations

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

Joshua Quick et al. Gigascience. .

Erratum in

Abstract

Background: The MinION™ is a new, portable single-molecule sequencer developed by Oxford Nanopore Technologies. It measures four inches in length and is powered from the USB 3.0 port of a laptop computer. The MinION™ measures the change in current resulting from DNA strands interacting with a charged protein nanopore. These measurements can then be used to deduce the underlying nucleotide sequence.

Findings: We present a read dataset from whole-genome shotgun sequencing of the model organism Escherichia coli K-12 substr. MG1655 generated on a MinION™ device during the early-access MinION™ Access Program (MAP). Sequencing runs of the MinION™ are presented, one generated using R7 chemistry (released in July 2014) and one using R7.3 (released in September 2014).

Conclusions: Base-called sequence data are provided to demonstrate the nature of data produced by the MinION™ platform and to encourage the development of customised methods for alignment, consensus and variant calling, de novo assembly and scaffolding. FAST5 files containing event data within the HDF5 container format are provided to assist with the development of improved base-calling methods.

Keywords: Genomics; Nanopore sequencing.

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Figures

Figure 1
Figure 1
Library preparation schematic for latest version of gDNA sequencing kit (SQK-MAP-003). Figure shows attachment sites for each of the two enzymes and tether.
Figure 2
Figure 2
The top row plots demonstrate collector’s curves of sequence reads over time measured in hours for the R7 (left) and R7.3 (right) run. Visible on the R7 run is a change in rate of read acquisition associated with topping-up the flowcell with additional library at hours 12, 24, 36 and 48. For the R7.3 run, the updated MinKNOW software reselects sequencing wells after 24 hours. The bottom row shows the histogram of read counts for reads shorter than 50,000 bp in length for the R7 (left) and R7.3 (right) run.
Figure 3
Figure 3
Kernel density plots showing accuracy for R7 and R7.3 chemistries with two different values for the LAST substitution penalty score.
Figure 4
Figure 4
Alignment identity and completeness. Each plot reflects the alignment identity and the proportion of the read aligned for all 2D reads, as well as the underlying template and complement sequences. The top two panels reflect the alignment results for normal and full 2D reads from the R7 flowcell, and the bottom two panels reflect the R7.3 flowcell. Left panels employ a mismatch penalty of 1 and right panels reflect a mismatch penalty of 2. Overall, the lower mismatch penalty increases the identity and fraction of the read that aligned and this effect is greatest for full 2D reads.
See this image and copyright information in PMC

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