Nicholas Loman | Search bioRxiv

bioRxiv2014

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

BackgroundThe 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 current produced when DNA strands translocate through and interact with a charged protein nanopore the device is able to deduce the underlying nucleotide sequence.\n\nFindingsWe 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).\n\nConclusionsBase-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. Datasets are provided through the GigaDB database http://gigadb.org/dataset/100102

Genomics↗

bioRxiv2014

Poretools: a toolkit for analyzing nanopore sequence data

Motivation: Nanopore sequencing may be the next disruptive technology in genomics. Nanopore sequencing has many attractive properties including the ability to detect single DNA molecules without prior amplification, the lack of reliance on expensive optical components, and the ability to sequence very long fragments. The MinION from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be commercialised and made available to early-access users. The MinION(TM) is a USB-connected, portable nanopore sequencer which permits real-time analysis of streaming event data. A cloud-based service is available to translate events into nucleotide base calls. However, software support to deal with such data is limited, and the community lacks a standardized toolkit for the analysis of nanopore datasets. Results: We introduce poretools, a flexible toolkit for manipulating and exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Poretools operates directly on the native FAST5 (a variant of the HDF5 standard) file format produced by ONT and provides a wealth of format conversion utilities and data exploration and visualization tools. Availability and implementation: Poretools is open source software and is written in Python as both a suite of command line utilities and a Python application programming interface. Source code and user documentation are freely available in Github at https://github.com/arq5x/poretools Contact: n.j.loman@bham.ac.uk, aaronquinlan@gmail.com Supplementary information: An IPython notebook demonstrating the use and functionality of poretools in greater detail is available from the Github repository.

Bioinformatics↗