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TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data

High-throughput sequencing is becoming a popular research tool but carries with it considerable costs in terms of computation time, data storage and bandwidth. Meanwhile, some research applications focusing on individual genes or pathways do not necessitate processing of a full sequencing dataset. T...

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Detalles Bibliográficos
Autores principales: Fimereli, Danai, Detours, Vincent, Konopka, Tomasz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627586/
https://www.ncbi.nlm.nih.gov/pubmed/23408855
http://dx.doi.org/10.1093/nar/gkt094
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author Fimereli, Danai
Detours, Vincent
Konopka, Tomasz
author_facet Fimereli, Danai
Detours, Vincent
Konopka, Tomasz
author_sort Fimereli, Danai
collection PubMed
description High-throughput sequencing is becoming a popular research tool but carries with it considerable costs in terms of computation time, data storage and bandwidth. Meanwhile, some research applications focusing on individual genes or pathways do not necessitate processing of a full sequencing dataset. Thus, it is desirable to partition a large dataset into smaller, manageable, but relevant pieces. We present a toolkit for partitioning raw sequencing data that includes a method for extracting reads that are likely to map onto pre-defined regions of interest. We show the method can be used to extract information about genes of interest from DNA or RNA sequencing samples in a fraction of the time and disk space required to process and store a full dataset. We report speedup factors between 2.6 and 96, depending on settings and samples used. The software is available at http://www.sourceforge.net/projects/triagetools/.
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spelling pubmed-36275862013-04-17 TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data Fimereli, Danai Detours, Vincent Konopka, Tomasz Nucleic Acids Res Methods Online High-throughput sequencing is becoming a popular research tool but carries with it considerable costs in terms of computation time, data storage and bandwidth. Meanwhile, some research applications focusing on individual genes or pathways do not necessitate processing of a full sequencing dataset. Thus, it is desirable to partition a large dataset into smaller, manageable, but relevant pieces. We present a toolkit for partitioning raw sequencing data that includes a method for extracting reads that are likely to map onto pre-defined regions of interest. We show the method can be used to extract information about genes of interest from DNA or RNA sequencing samples in a fraction of the time and disk space required to process and store a full dataset. We report speedup factors between 2.6 and 96, depending on settings and samples used. The software is available at http://www.sourceforge.net/projects/triagetools/. Oxford University Press 2013-04 2013-02-12 /pmc/articles/PMC3627586/ /pubmed/23408855 http://dx.doi.org/10.1093/nar/gkt094 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Fimereli, Danai
Detours, Vincent
Konopka, Tomasz
TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data
title TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data
title_full TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data
title_fullStr TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data
title_full_unstemmed TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data
title_short TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data
title_sort triagetools: tools for partitioning and prioritizing analysis of high-throughput sequencing data
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627586/
https://www.ncbi.nlm.nih.gov/pubmed/23408855
http://dx.doi.org/10.1093/nar/gkt094
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