ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility

Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil / Fundação Ataulpho de Paiva. Rio de Janeiro, RJ, Brasil.

Detalles Bibliográficos
Autores: Otto, T. D., Vasconcellos, E. A., Gomes, L. H. F., Moreira, A. S., Degrave, Win M., Lima, L. Mendonça, Ferreira, M. Alves
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2008
País:Brasil
Institución:Fundação Oswaldo Cruz (FIOCRUZ)
Repositorio:Repositório Institucional da FIOCRUZ (ARCA)
Idioma:inglés
OAI Identifier:oai:arca.fiocruz.br:icict/32365
Acceso en línea:https://arca.fiocruz.br/handle/icict/32365
Access Level:acceso abierto
Palabra clave:Processamento Cromatográfico
Sequenciamento de DNA
Pipeline de sequenciamento
Sequencing pipeline
Chromatogram processing
DNA sequencing
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dc.title.none.fl_str_mv ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility
title ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility
spellingShingle ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility
Otto, T. D.
Processamento Cromatográfico
Sequenciamento de DNA
Pipeline de sequenciamento
Sequencing pipeline
Chromatogram processing
DNA sequencing
title_short ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility
title_full ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility
title_fullStr ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility
title_full_unstemmed ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility
title_sort ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility
dc.creator.none.fl_str_mv Otto, T. D.
Vasconcellos, E. A.
Gomes, L. H. F.
Moreira, A. S.
Degrave, Win M.
Lima, L. Mendonça
Ferreira, M. Alves
author Otto, T. D.
author_facet Otto, T. D.
Vasconcellos, E. A.
Gomes, L. H. F.
Moreira, A. S.
Degrave, Win M.
Lima, L. Mendonça
Ferreira, M. Alves
author_role author
author2 Vasconcellos, E. A.
Gomes, L. H. F.
Moreira, A. S.
Degrave, Win M.
Lima, L. Mendonça
Ferreira, M. Alves
author2_role author
author
author
author
author
author
dc.subject.other.none.fl_str_mv Processamento Cromatográfico
Sequenciamento de DNA
Pipeline de sequenciamento
topic Processamento Cromatográfico
Sequenciamento de DNA
Pipeline de sequenciamento
Sequencing pipeline
Chromatogram processing
DNA sequencing
dc.subject.en.none.fl_str_mv Sequencing pipeline
Chromatogram processing
DNA sequencing
description Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil / Fundação Ataulpho de Paiva. Rio de Janeiro, RJ, Brasil.
publishDate 2008
dc.date.issued.fl_str_mv 2008
dc.date.accessioned.fl_str_mv 2019-04-04T14:14:50Z
dc.date.available.fl_str_mv 2019-04-04T14:14:50Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv OTTO, Thomas D. et al. ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility. Genet. Mol. Res., v. 7, n. 3, p. 861-871, 2008.
dc.identifier.uri.fl_str_mv https://arca.fiocruz.br/handle/icict/32365
dc.identifier.issn.none.fl_str_mv 1676-5680
identifier_str_mv OTTO, Thomas D. et al. ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility. Genet. Mol. Res., v. 7, n. 3, p. 861-871, 2008.
1676-5680
url https://arca.fiocruz.br/handle/icict/32365
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Fundação de Pesquisas de Ribeirão Preto
publisher.none.fl_str_mv Fundação de Pesquisas de Ribeirão Preto
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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spelling 2019-04-04T14:14:50Z2019-04-04T14:14:50Z2008OTTO, Thomas D. et al. ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility. Genet. Mol. Res., v. 7, n. 3, p. 861-871, 2008.1676-5680https://arca.fiocruz.br/handle/icict/32365engFundação de Pesquisas de Ribeirão PretoProcessamento CromatográficoSequenciamento de DNAPipeline de sequenciamentoSequencing pipelineChromatogram processingDNA sequencingChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facilityinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil / Fundação Ataulpho de Paiva. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil / Fundação Ataulpho de Paiva. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil / Universidade Federal do Rio de Janeiro. Faculdade de Medicina. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil.Optimizing and monitoring the data flow in high-throughput sequencing facilities is important for data input and output, for tracking the status of results for the users of the facility, and to guarantee a good, high-quality service. In a multi-user system environment with different throughputs, each user wants to access his/her data easily, track his/her sequencing history, analyze sequences and their quality, and apply some basic post-sequencing analysis, without the necessity of installing further software. Recently, Fiocruz established such a core facility as a "technological platform". Infrastructure includes a 48-capillary 3730 DNA Sequence Analyzer (Applied Biosystems) and supporting equipment. The service includes running samples for large-scale users, performing DNA sequencing reactions and runs for medium and small users, and participation in partial or full genome projects. We implemented a workflow that fulfills these requirements for small and high throughput users. Our implementation also includes the monitoring of data for continuous quality improvement (reports by plate, month and user) by the sequencing staff. For the user, different analyses of the chromatograms, such as visualization of good quality regions, as well as processing, such as comparisons or assemblies, are available. So far, 180 users have made use of the service, generating 155,000 sequences, 35% of which were produced for the BCG Moreau-RJ genome project.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZOtto, T. D.Vasconcellos, E. A.Gomes, L. H. F.Moreira, A. S.Degrave, Win M.Lima, L. MendonçaFerreira, M. 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