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fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data
BACKGROUND: Next generation sequencing datasets are stored as FASTQ formatted files. In order to avoid downstream artefacts, it is critical to implement a robust preprocessing protocol of the FASTQ sequence in order to determine the integrity and quality of the data. RESULTS: Here I describe fastQ_b...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2017
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5508660/ https://www.ncbi.nlm.nih.gov/pubmed/28701181 http://dx.doi.org/10.1186/s13104-017-2616-7 |
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author | O’Halloran, Damien M. |
author_facet | O’Halloran, Damien M. |
author_sort | O’Halloran, Damien M. |
collection | PubMed |
description | BACKGROUND: Next generation sequencing datasets are stored as FASTQ formatted files. In order to avoid downstream artefacts, it is critical to implement a robust preprocessing protocol of the FASTQ sequence in order to determine the integrity and quality of the data. RESULTS: Here I describe fastQ_brew which is a package that provides a suite of methods to evaluate sequence data in FASTQ format and efficiently implements a variety of manipulations to filter sequence data by size, quality and/or sequence. fastQ_brew allows for mismatch searches to adapter sequences, left and right end trimming, removal of duplicate reads, as well as reads containing non-designated bases. fastQ_brew also returns summary statistics on the unfiltered and filtered FASTQ data, and offers FASTQ to FASTA conversion as well as FASTQ reverse complement and DNA to RNA manipulations. CONCLUSIONS: fastQ_brew is open source and freely available to all users at the following webpage: https://github.com/dohalloran/fastQ_brew. |
format | Online Article Text |
id | pubmed-5508660 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-55086602017-07-17 fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data O’Halloran, Damien M. BMC Res Notes Technical Note BACKGROUND: Next generation sequencing datasets are stored as FASTQ formatted files. In order to avoid downstream artefacts, it is critical to implement a robust preprocessing protocol of the FASTQ sequence in order to determine the integrity and quality of the data. RESULTS: Here I describe fastQ_brew which is a package that provides a suite of methods to evaluate sequence data in FASTQ format and efficiently implements a variety of manipulations to filter sequence data by size, quality and/or sequence. fastQ_brew allows for mismatch searches to adapter sequences, left and right end trimming, removal of duplicate reads, as well as reads containing non-designated bases. fastQ_brew also returns summary statistics on the unfiltered and filtered FASTQ data, and offers FASTQ to FASTA conversion as well as FASTQ reverse complement and DNA to RNA manipulations. CONCLUSIONS: fastQ_brew is open source and freely available to all users at the following webpage: https://github.com/dohalloran/fastQ_brew. BioMed Central 2017-07-12 /pmc/articles/PMC5508660/ /pubmed/28701181 http://dx.doi.org/10.1186/s13104-017-2616-7 Text en © The Author(s) 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Technical Note O’Halloran, Damien M. fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data |
title | fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data |
title_full | fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data |
title_fullStr | fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data |
title_full_unstemmed | fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data |
title_short | fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data |
title_sort | fastq_brew: module for analysis, preprocessing, and reformatting of fastq sequence data |
topic | Technical Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5508660/ https://www.ncbi.nlm.nih.gov/pubmed/28701181 http://dx.doi.org/10.1186/s13104-017-2616-7 |
work_keys_str_mv | AT ohallorandamienm fastqbrewmoduleforanalysispreprocessingandreformattingoffastqsequencedata |