DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing

Detalhes bibliográficos
Autor(a) principal: Mendes, Catarina Inês
Data de Publicação: 2020
Outros Autores: Lizarazo, Erley, Machado, Miguel P., Silva, Diogo N., Tami, Adriana, Ramirez, Mário, Couto, Natacha, Rossen, John W. A., Carrico, Joao Andre
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/49903
Resumo: © 2020 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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spelling DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencingContainerizationDengue virusMetagenomicsReproducibilityScalabilitySurveillanceWorkflow© 2020 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License.Dengue virus (DENV) represents a public health threat and economic burden in affected countries. The availability of genomic data is key to understanding viral evolution and dynamics, supporting improved control strategies. Currently, the use of high-throughput sequencing (HTS) technologies, which can be applied both directly to patient samples (shotgun metagenomics) and to PCR-amplified viral sequences (amplicon sequencing), is potentially the most informative approach to monitor viral dissemination and genetic diversity by providing, in a single methodological step, identification and characterization of the whole viral genome at the nucleotide level. Despite many advantages, these technologies require bioinformatics expertise and appropriate infrastructure for the analysis and interpretation of the resulting data. In addition, the many software solutions available can hamper the reproducibility and comparison of results. Here we present DEN-IM, a one-stop, user-friendly, containerized and reproducible workflow for the analysis of DENV short-read sequencing data from both amplicon and shotgun metagenomics approaches. It is able to infer the DENV coding sequence (CDS), identify the serotype and genotype, and generate a phylogenetic tree. It can easily be run on any UNIX-like system, from local machines to high-performance computing clusters, performing a comprehensive analysis without the requirement for extensive bioinformatics expertise. Using DEN-IM, we successfully analysed two types of DENV datasets. The first comprised 25 shotgun metagenomic sequencing samples from patients with variable serotypes and genotypes, including an in vitro spiked sample containing the four known serotypes. The second consisted of 106 paired-end and 76 single-end amplicon sequences of DENV 3 genotype III and DENV 1 genotype I, respectively, where DEN-IM allowed detection of the intra-genotype diversity. The DEN-IM workflow, parameters and execution configuration files, and documentation are freely available at https://github.com/B-UMMI/DEN-IM).C. I. M. was supported by the Fundação para a Ciência e Tecnologia (grant SFRH/BD/129483/2017). E. L. received a Abel Tasman Talent Program grant from the UMCG, University of Groningen, Groningen, The Netherlands. This work was partly supported by the ONEIDA project (LISBOA-01–0145-FEDER-016417) co-funded by FEEI–Fundos Europeus Estruturais e de Investimento from Programa Operacional Regional Lisboa 2020 and by national funds from FCT–Fundação para a Ciência e a Tecnologia and by UID/BIM/50005/2019, project funded by Fundação para a Ciência e a Tecnologia (FCT)/ Ministério da Ciência, Tecnologia e Ensino Superior (MCTES) through Fundos do Orçamento de Estado.Microbiology SocietyRepositório da Universidade de LisboaMendes, Catarina InêsLizarazo, ErleyMachado, Miguel P.Silva, Diogo N.Tami, AdrianaRamirez, MárioCouto, NatachaRossen, John W. A.Carrico, Joao Andre2021-10-15T13:31:43Z20202020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/49903engMicrob Genom. 2020 Mar;6(3):e00032810.1099/mgen.0.0003282057-5858info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T16:53:52Zoai:repositorio.ul.pt:10451/49903Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:01:25.798872Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
title DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
spellingShingle DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
Mendes, Catarina Inês
Containerization
Dengue virus
Metagenomics
Reproducibility
Scalability
Surveillance
Workflow
title_short DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
title_full DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
title_fullStr DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
title_full_unstemmed DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
title_sort DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
author Mendes, Catarina Inês
author_facet Mendes, Catarina Inês
Lizarazo, Erley
Machado, Miguel P.
Silva, Diogo N.
Tami, Adriana
Ramirez, Mário
Couto, Natacha
Rossen, John W. A.
Carrico, Joao Andre
author_role author
author2 Lizarazo, Erley
Machado, Miguel P.
Silva, Diogo N.
Tami, Adriana
Ramirez, Mário
Couto, Natacha
Rossen, John W. A.
Carrico, Joao Andre
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Mendes, Catarina Inês
Lizarazo, Erley
Machado, Miguel P.
Silva, Diogo N.
Tami, Adriana
Ramirez, Mário
Couto, Natacha
Rossen, John W. A.
Carrico, Joao Andre
dc.subject.por.fl_str_mv Containerization
Dengue virus
Metagenomics
Reproducibility
Scalability
Surveillance
Workflow
topic Containerization
Dengue virus
Metagenomics
Reproducibility
Scalability
Surveillance
Workflow
description © 2020 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020-01-01T00:00:00Z
2021-10-15T13:31:43Z
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.uri.fl_str_mv http://hdl.handle.net/10451/49903
url http://hdl.handle.net/10451/49903
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Microb Genom. 2020 Mar;6(3):e000328
10.1099/mgen.0.000328
2057-5858
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Microbiology Society
publisher.none.fl_str_mv Microbiology Society
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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