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Winter 2015

British bioinformatics at the forefront of nanopore sequencing

Copyright: Oxford Nanopore Technologies

In 2012, the British company Oxford Nanopore Technologies (ONT) presented a tiny DNA sequencer that plugs into a USB port and sequence DNA directly from blood using an engineered nanopore. Analysing its data is the next step in portable sequencing.

BBSRC-funded training grants have played an important part in demonstrating that biological nanopores could differentiate between the individual DNA bases in a single DNA molecule - a key aspect of the sequencing methods developed by ONT. As a mobile sequencing device powered by the USB port of a laptop, the MinION has a huge range of potential applications. But while these miniature machines have been pitched to 'revolutionise many areas of biology and medicine', the data outputs have some issues that require specific software. British scientists are stepping in to offer accessible solutions.

While the MinION system is not widely available, it has been distributed for early-access and testing. Early reports suggest that it is capable of reading very long single molecule DNA sequences with sufficient quality to be useful, although not yet as accurately as those produced by some more mature technologies.

However, the research community is faced with a number of informatics challenges and currently lacks a standardised toolkit for the analysis of nanopore datasets.

Mick Watson, Edinburgh Genomics, The Roslin Institute, explains: "The MinION outputs binary files in a format called HDF5. These contain raw data from the sequencer, which are then processed by a cloud-based system called 'metrichor'. This produces another set of files in an HDF5 format. It is not uncommon for users to be presented with tens of thousands of HDF5 files with no software with which to access the data. Furthermore, data is stored in a single directory, with no subdirectories, and users find themselves needing to manipulate thousands of files manually, which takes time and is error-prone."

Mick has produced software tools specifically for this, "We have developed poRe, a package which enables users to manipulate MinION files into separate folders, extract files, gather statistics and plot a number of key graphs."

As MinION users rely on a high-specification Windows laptop, Watson has ensured compatibility. The Windows version enables users to run poRe on the MinION laptop itself, rather than copying the data to a Linux server to process with Perl or Python. This key feature brings users closer to true mobile DNA sequencing.

In addition to this BBSRC and NERC funded software, MRC have funded Dr Nick Loman at University of Birmingham to provide a flexible toolkit for exploring datasets generated by MinION. Poretools provides a wealth of format conversion utilities, data exploration and visualization tools.

Notes to editors

The papers:

  • Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics. DOI: 10.1093/bioinformatics/btu555
  • poRe: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics DOI: 10.1093/bioinformatics/btu590