Abstract
Motivation: Nanopore sequencing may be the next disruptive technology in genomics, owing to its ability to detect single DNA molecules without prior amplification, lack of reliance on expensive optical components, and the ability to sequence long fragments. The MinION™ from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be commercialized and is now available to early-access users. The MinION™ is a USB-connected, portable nanopore sequencer that permits real-time analysis of streaming event data. Currently, the research community lacks a standardized toolkit for the analysis of nanopore datasets.Results: We introduce poretools, a flexible toolkit for 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 (an application 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 an open-source software and is written in Python as both a suite of command line utilities and a Python application programming interface. Source code is freely available in Github at https://www.github.com/arq5x/poretoolsContact: n.j.loman@bham.ac.uk and aaronquinlan@gmail.comSupplementary information: An IPython notebook demonstrating the functionality of poretools is in Github. Complete documentation is available at http://poretools.readthedocs.org.
Highlights
The idea of using biological nanopores for DNA sequencing was proposed almost twenty years ago (Church et al (1995); Kasianowicz et al (1996))
Single molecule detection and the absence of a prior amplification step means that extremely long fragments can be sequenced without any loss in quality
The most fundamental requirement provided by poretools is the ability to convert the sequencing data resulting from a MinION run from HDF5/FAST5 format to either FASTA or FASTQ format in order to facilitate analyses with sequence alignment and/or assembly software
Summary
The idea of using biological nanopores for DNA sequencing was proposed almost twenty years ago (Church et al (1995); Kasianowicz et al (1996)). This approach relies on the direct, electrical detection of single DNA strands in contact with an individual pore. Single molecule detection and the absence of a prior amplification step means that extremely long fragments can be sequenced without any loss in quality. In May 2014, Oxford Nanopore Technologies released MinIONTM, the first commercially-available nanopore DNA sequencing device
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