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Poretools: a toolkit for analyzing nanopore sequence data

Nicholas J. Loman, Aaron R. Quinlan
doi: https://doi.org/10.1101/007401
Nicholas J. Loman
1Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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Aaron R. Quinlan
2Departments of Public Health Sciences and Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
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ABSTRACT

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 is now available to early-access users. The MinION™ 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

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 23, 2014.
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Poretools: a toolkit for analyzing nanopore sequence data
Nicholas J. Loman, Aaron R. Quinlan
bioRxiv 007401; doi: https://doi.org/10.1101/007401
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Poretools: a toolkit for analyzing nanopore sequence data
Nicholas J. Loman, Aaron R. Quinlan
bioRxiv 007401; doi: https://doi.org/10.1101/007401

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