Bacterial whole-genome read data from the Oxford Nanopore Technologies MinION™ nanopore sequencer.
Dataset type: Genomic
Data released on September 10, 2014
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. By measuring the change in resistance produced when DNA strands translocate through and interact with a protein nanopore the device is able to deduce the underlying nucleotide sequence.
Here 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 with R7 chemistry during the early-access MinION Access Program (MAP).
Three sequencing runs of the MinION were performed using R7 chemistry. The first run produced 43,656 forward reads (272Mb), 23,338 (125Mb) reverse reads, 20,087 two-direction (2D) reads (131Mb), of which 8% (10Mb) were full 2D. Full 2D reads means that the complementary strand was successfully slowed through the pore.
The R7 protocol has a modification to increase the relative number of full 2D reads (NONI). To exploit this, two new libraries were produced which included an overnight incubation stage (ONI-1 and ONI-2). Each library was run on an individual flow cell. This resulted in 6,534 & 8,260 forward reads, 2,171 & 2,945 reads and 1,740 & 2,394 2D reads (27%, 29%). In this case, 50% and 41.8% of reads were full 2D respectively. The mean fragment lengths for 2D reads from the three libraries were 6,543 (NONI) 6,907 (ONI-1) and 6,434 (ONI-2).
A fourth run was performed using a further modified chemistry (R7.3), which resulted in 39819 forward reads, 18889 complement reads, of which 11823 and 9563 were 2D and full 2D respectively.
Raw and assembled sequence data is provided to demonstrate the nature of data produced by the MinION™ platform and to encourage the development of customised methods for alignment 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.
Read the peer-reviewed publication(s):
Quick, J., Quinlan, A. R., & Loman, N. J. (2014). A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer. GigaScience, 3(1). doi:10.1186/2047-217x-3-22
Accessions (data referenced by this study):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|Ecoli_K12_MG1655||511145||E.coli||E.coli|| Estimated genome size:4.6|
Nucleic acid extraction:Invisorb Spin Cell Mini Ki...
Sample collection device or method:L-shaped spread...
... Estimated genome size:4.6
Nucleic acid extraction:Invisorb Spin Cell Mini Kit (Invitek, Birkenfeld, Germany), following manufacturers protocol for extraction from serum and plasma.
Sample collection device or method:L-shaped spreader
Sequencing method:MinION (Oxford Nanopore Technologies), R7 chemistry
Description:DNA sample prepared for Nanopore sequence run