FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files

Autores
Roser, Leandro Gabriel; Agüero, Fernán Gonzalo; Sanchez, Daniel Oscar
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.Results This paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.Conclusions FastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.
Fil: Roser, Leandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
Fil: Agüero, Fernán Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
Fil: Sanchez, Daniel Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
Materia
FASTQ
BIOCONDUCTOR
FASTQCLEANER
QUALITY CONTROL
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/101277
Acceder
id CONICETDig_2a33a6fcf5e98d575939eb515795356f
oai_identifier_str oai:ri.conicet.gov.ar:11336/101277
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ filesRoser, Leandro GabrielAgüero, Fernán GonzaloSanchez, Daniel OscarFASTQBIOCONDUCTORFASTQCLEANERQUALITY CONTROLhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Background Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.Results This paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.Conclusions FastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.Fil: Roser, Leandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Agüero, Fernán Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Sanchez, Daniel Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaCold Spring Harbor Laboratory Press2018-08-28info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/101277Roser, Leandro Gabriel; Agüero, Fernán Gonzalo; Sanchez, Daniel Oscar; FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files; Cold Spring Harbor Laboratory Press; bioRxiv; 361; 28-8-2018; 1-241476-4687CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/10.1101/393140v3info:eu-repo/semantics/altIdentifier/doi/10.1101/393140info:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2961-8info:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-019-2961-8info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-01-08T12:49:27Zoai:ri.conicet.gov.ar:11336/101277instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982026-01-08 12:49:27.434CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
title FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
spellingShingle FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
Roser, Leandro Gabriel
FASTQ
BIOCONDUCTOR
FASTQCLEANER
QUALITY CONTROL
title_short FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
title_full FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
title_fullStr FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
title_full_unstemmed FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
title_sort FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
dc.creator.none.fl_str_mv Roser, Leandro Gabriel
Agüero, Fernán Gonzalo
Sanchez, Daniel Oscar
author Roser, Leandro Gabriel
author_facet Roser, Leandro Gabriel
Agüero, Fernán Gonzalo
Sanchez, Daniel Oscar
author_role author
author2 Agüero, Fernán Gonzalo
Sanchez, Daniel Oscar
author2_role author
author
dc.subject.none.fl_str_mv FASTQ
BIOCONDUCTOR
FASTQCLEANER
QUALITY CONTROL
topic FASTQ
BIOCONDUCTOR
FASTQCLEANER
QUALITY CONTROL
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.Results This paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.Conclusions FastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.
Fil: Roser, Leandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
Fil: Agüero, Fernán Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
Fil: Sanchez, Daniel Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
description Background Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.Results This paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.Conclusions FastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.
publishDate 2018
dc.date.none.fl_str_mv 2018-08-28
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/101277
Roser, Leandro Gabriel; Agüero, Fernán Gonzalo; Sanchez, Daniel Oscar; FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files; Cold Spring Harbor Laboratory Press; bioRxiv; 361; 28-8-2018; 1-24
1476-4687
CONICET Digital
CONICET
url http://hdl.handle.net/11336/101277
identifier_str_mv Roser, Leandro Gabriel; Agüero, Fernán Gonzalo; Sanchez, Daniel Oscar; FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files; Cold Spring Harbor Laboratory Press; bioRxiv; 361; 28-8-2018; 1-24
1476-4687
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/10.1101/393140v3
info:eu-repo/semantics/altIdentifier/doi/10.1101/393140
info:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2961-8
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-019-2961-8
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1853775122246139904
score 13.25844

Publicaciones similares