poRe GUIs for parallel and real-time processing of MinION sequence data

Robert Stewart; Mick Watson

doi:10.1093/bioinformatics/btx136

poRe GUIs for parallel and real-time processing of MinION sequence data

Research output: Contribution to journal › Article › peer-review

Abstract

Motivation: Oxford Nanopore's MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. The nature of the MinION output requires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs.

Results: We have developed two GUIs for the R package poRe that allow parallel and real-time processing of MinION datasets. Both GUIs are capable of extracting sequence- and meta- data from large MinION datasets via a friendly point-and-click interface using commodity hardware.

Availability: The GUIs are packaged within poRe which is available on SourceForge: https://sourceforge.net/projects/rpore/files/ .

Documentation is available on GitHub: https://github.com/mw55309/poRe_docs.

Contact: [email protected].

Supplementary information: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	2207-2208
Journal	Bioinformatics
Volume	33
Issue number	14
Early online date	9 Mar 2017
DOIs	https://doi.org/10.1093/bioinformatics/btx136
Publication status	Published - 15 Jul 2017

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10.1093/bioinformatics/btx136

poRe GUIs for parallel and real-time processing of MinION sequence data
© The Author(s) 2017 . Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 241 KBLicence: Creative Commons: Attribution (CC-BY)

ISP 1 2017/22 Blueprints for Healthy Animals
Watson, M. (Principal Investigator)
BBSRC
1/04/17 → 31/03/22
Project: Research
poRe: visualization and analysis of nanopore sequencing data for rapid and mobile pathogen detection
Watson, M. (Principal Investigator)
BBSRC
1/07/15 → 31/12/16
Project: Research
Ark Genomics
Watson, M. (Principal Investigator), Archibald, A. (Co-investigator) & Burt, D. (Co-investigator)
BBSRC
1/04/12 → 31/03/17
Project: Research

Cite this

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abstract = "Motivation: Oxford Nanopore's MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. The nature of the MinION output requires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs.Results: We have developed two GUIs for the R package poRe that allow parallel and real-time processing of MinION datasets. Both GUIs are capable of extracting sequence- and meta- data from large MinION datasets via a friendly point-and-click interface using commodity hardware.Availability: The GUIs are packaged within poRe which is available on SourceForge: https://sourceforge.net/projects/rpore/files/ .Documentation is available on GitHub: https://github.com/mw55309/poRe_docs.Contact: [email protected] information: Supplementary data are available at Bioinformatics online.",

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poRe GUIs for parallel and real-time processing of MinION sequence data

Abstract

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Projects

ISP 1 2017/22 Blueprints for Healthy Animals

poRe: visualization and analysis of nanopore sequencing data for rapid and mobile pathogen detection

Ark Genomics

Cite this