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

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...

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Detalles Bibliográficos
Autores principales: Stewart, Robert D, Watson, Mick
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870607/
https://www.ncbi.nlm.nih.gov/pubmed/28334395
http://dx.doi.org/10.1093/bioinformatics/btx136
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author Stewart, Robert D
Watson, Mick
author_facet Stewart, Robert D
Watson, Mick
author_sort Stewart, Robert D
collection PubMed
description 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 AND IMPLEMENTATION: 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.
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spelling pubmed-58706072018-04-05 poRe GUIs for parallel and real-time processing of MinION sequence data Stewart, Robert D Watson, Mick Bioinformatics Applications Notes 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 AND IMPLEMENTATION: 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. Oxford University Press 2017-07-15 2017-03-09 /pmc/articles/PMC5870607/ /pubmed/28334395 http://dx.doi.org/10.1093/bioinformatics/btx136 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ 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.
spellingShingle Applications Notes
Stewart, Robert D
Watson, Mick
poRe GUIs for parallel and real-time processing of MinION sequence data
title poRe GUIs for parallel and real-time processing of MinION sequence data
title_full poRe GUIs for parallel and real-time processing of MinION sequence data
title_fullStr poRe GUIs for parallel and real-time processing of MinION sequence data
title_full_unstemmed poRe GUIs for parallel and real-time processing of MinION sequence data
title_short poRe GUIs for parallel and real-time processing of MinION sequence data
title_sort pore guis for parallel and real-time processing of minion sequence data
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870607/
https://www.ncbi.nlm.nih.gov/pubmed/28334395
http://dx.doi.org/10.1093/bioinformatics/btx136
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