4.7 Article

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

Journal

GIGASCIENCE
Volume 3, Issue -, Pages -

Publisher

BIOMED CENTRAL LTD
DOI: 10.1186/2047-217X-3-22

Keywords

Genomics; Nanopore sequencing

Funding

  1. Medical Research Council Special Training Fellowship in Biomedical Informatics
  2. National Institute for Health research (NIHR) Surgical Reconstruction and Microbiology Research Centre
  3. University Hospitals Birmingham NHS Foundation Trust
  4. University of Birmingham
  5. Royal Centre for Defence Medicine
  6. NIH (NGHRI) [1R01HG006693-01]
  7. MRC [MR/J014370/1] Funding Source: UKRI
  8. Medical Research Council [MR/J014370/1] Funding Source: researchfish

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Background: The MinION (TM) 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 (TM) 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 (TM) device during the early-access MinION (TM) Access Program (MAP). Sequencing runs of the MinION (TM) 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 (TM) 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.

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