Poretools: a toolkit for analyzing nanopore sequence data

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Poretools : a toolkit for analyzing nanopore sequence data. / Loman, Nicholas J; Quinlan, Aaron R.

In: Bioinformatics, Vol. 30, No. 23, 01.12.2014, p. 3399-401.

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Loman, Nicholas J ; Quinlan, Aaron R. / Poretools : a toolkit for analyzing nanopore sequence data. In: Bioinformatics. 2014 ; Vol. 30, No. 23. pp. 3399-401.

Bibtex

@article{27ad9bd9e2e8432387fab3c7723a235a,
title = "Poretools: a toolkit for analyzing nanopore sequence data",
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{\texttrademark} from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be commercialized and is now available to early-access users. The MinION{\texttrademark} 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{\texttrademark} 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/poretools.",
keywords = "Nanopores, Sequence Analysis, DNA, Software",
author = "Loman, {Nicholas J} and Quinlan, {Aaron R}",
note = "{\textcopyright} The Author 2014. Published by Oxford University Press.",
year = "2014",
month = dec,
day = "1",
doi = "10.1093/bioinformatics/btu555",
language = "English",
volume = "30",
pages = "3399--401",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "23",

}

RIS

TY - JOUR

T1 - Poretools

T2 - a toolkit for analyzing nanopore sequence data

AU - Loman, Nicholas J

AU - Quinlan, Aaron R

N1 - © The Author 2014. Published by Oxford University Press.

PY - 2014/12/1

Y1 - 2014/12/1

N2 - 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/poretools.

AB - 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/poretools.

KW - Nanopores

KW - Sequence Analysis, DNA

KW - Software

U2 - 10.1093/bioinformatics/btu555

DO - 10.1093/bioinformatics/btu555

M3 - Article

C2 - 25143291

VL - 30

SP - 3399

EP - 3401

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 23

ER -