Oxford Nanopore MinION Data from E.Coli K-12 Genome is here

Oxford Nanopore MinION

Oxford Nanopore MinION (Image: Nick Loman)

The wait is over. The long sought after data from Oxford Nanopore is here. Almost three months ago, we got a glimpse of a single read from Nick Loman. Now, Nick Loman organizing the really awesome Nanopore themed Google Hangout and announced that Oxford Nanopore MinION data from E.Coli K 12 substrain.

The E. coli genome data from Nanopore MinION data is available from GigaDB. In addition to directly downloading the data from Gigadb, one can also download using Aspera.

The raw data is about 80 Gb in size, while processed data in fasta format is about 180Mb and easy to download..

Bacterial whole-genome read data from the Oxford Nanopore Technologies MinION™ nanopore sequencer.

Quick, J; Loman N.J (2014): Bacterial whole-genome read data from the Oxford Nanopore Technologies MinION™ nanopore sequencer. GigaScience Database. http://dx.doi.org/10.5524/100102

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).
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.

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