Benchmarking different approaches for Norovirus genome assembly in metagenome samples

Detalhes bibliográficos
Autor(a) principal: Fuentes-Trillo, Azahara
Data de Publicação: 2021
Outros Autores: Monzó, Carolina, Manzano, Iris, Santiso-Bellón, Cristina, Andrade, Juliana da Silva Ribeiro de, Gozalbo-Rovira, Roberto, García-García, Ana-Bárbara, Rodríguez-Díaz, Jesús, Chaves, Felipe Javier
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/50884
Resumo: Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain. Spain.
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spelling Fuentes-Trillo, AzaharaMonzó, CarolinaManzano, IrisSantiso-Bellón, CristinaAndrade, Juliana da Silva Ribeiro deGozalbo-Rovira, RobertoGarcía-García, Ana-BárbaraRodríguez-Díaz, JesúsChaves, Felipe Javier2022-01-25T19:08:37Z2022-01-25T19:08:37Z2021FUENTES-TRILLO, Azahara et al. Benchmarking different approaches for Norovirus genome assembly in metagenome samples. BMC Genomics, v. 22, 849, p. 1 - 12, 2021.1471-2164https://www.arca.fiocruz.br/handle/icict/5088410.1186/s12864-021-08067-2engBMCNorovírusMontagem de novo do genomaMetagenômicaNorovirusGenome de-novo assemblyMetagenomicsBenchmarking different approaches for Norovirus genome assembly in metagenome samplesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUnit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain. Spain.Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain. Spain.Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain. Spain.Department of Microbiology, School of Medicine. University of Valencia, Valencia, Spain.Fundação Oswaldo Cruz. Insituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro. RJ, Brasil. , RJ, Brasil.Department of Microbiology, School of Medicine. University of Valencia, Valencia, Spain.FUENTES-TUnit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain. Spain / 4Spanish Biomedical Research Network in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.Department of Microbiology, School of Medicine. University of Valencia, Valencia, Spain.Department of Microbiology, School of Medicine. University of Valencia, Valencia, Spain / Spanish Biomedical Research Network in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain / Sequecing Multiplex S.L., Valencia, Spain.Background: Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains. Furthermore, there is no standard method for obtaining whole-genome sequences in nonrelated patients. After polyA RNA isolation and sequencing in eight patients with acute gastroenteritis, we evaluated two de Bruijn graph assemblers (SPAdes and MEGAHIT), combined with four different and common pre-assembly strategies, and compared those yielding whole genome Norovirus contigs. Results: Reference-genome guided strategies with both host and target virus did not present any advantages compared to the assembly of non-filtered data in the case of SPAdes, and in the case of MEGAHIT, only host genome filtering presented improvements. MEGAHIT performed better than SPAdes in most samples, reaching complete genome sequences in most of them for all the strategies employed. Read binning with CD-HIT improved assembly when paired with different analysis strategies, and more notably in the case of SPAdes. Conclusions: Not all metagenome assemblies are equal and the choice in the workflow depends on the species studied and the prior steps to analysis. We may need different approaches even for samples treated equally due to the presence of high intra host variability. We tested and compared different workflows for the accurate assembly of Norovirus genomes and established their assembly capacities for this purpose.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/50884/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALJulianaRS_Andrade_etal_IOC_2021.pdfJulianaRS_Andrade_etal_IOC_2021.pdfapplication/pdf971262https://www.arca.fiocruz.br/bitstream/icict/50884/2/JulianaRS_Andrade_etal_IOC_2021.pdfcdd68f411ddec237d4d8c49faa0989afMD52icict/508842022-01-25 16:08:37.822oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352022-01-25T19:08:37Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title Benchmarking different approaches for Norovirus genome assembly in metagenome samples
spellingShingle Benchmarking different approaches for Norovirus genome assembly in metagenome samples
Fuentes-Trillo, Azahara
Norovírus
Montagem de novo do genoma
Metagenômica
Norovirus
Genome de-novo assembly
Metagenomics
title_short Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title_full Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title_fullStr Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title_full_unstemmed Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title_sort Benchmarking different approaches for Norovirus genome assembly in metagenome samples
author Fuentes-Trillo, Azahara
author_facet Fuentes-Trillo, Azahara
Monzó, Carolina
Manzano, Iris
Santiso-Bellón, Cristina
Andrade, Juliana da Silva Ribeiro de
Gozalbo-Rovira, Roberto
García-García, Ana-Bárbara
Rodríguez-Díaz, Jesús
Chaves, Felipe Javier
author_role author
author2 Monzó, Carolina
Manzano, Iris
Santiso-Bellón, Cristina
Andrade, Juliana da Silva Ribeiro de
Gozalbo-Rovira, Roberto
García-García, Ana-Bárbara
Rodríguez-Díaz, Jesús
Chaves, Felipe Javier
author2_role author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Fuentes-Trillo, Azahara
Monzó, Carolina
Manzano, Iris
Santiso-Bellón, Cristina
Andrade, Juliana da Silva Ribeiro de
Gozalbo-Rovira, Roberto
García-García, Ana-Bárbara
Rodríguez-Díaz, Jesús
Chaves, Felipe Javier
dc.subject.other.pt_BR.fl_str_mv Norovírus
Montagem de novo do genoma
Metagenômica
topic Norovírus
Montagem de novo do genoma
Metagenômica
Norovirus
Genome de-novo assembly
Metagenomics
dc.subject.en.pt_BR.fl_str_mv Norovirus
Genome de-novo assembly
Metagenomics
description Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain. Spain.
publishDate 2021
dc.date.issued.fl_str_mv 2021
dc.date.accessioned.fl_str_mv 2022-01-25T19:08:37Z
dc.date.available.fl_str_mv 2022-01-25T19:08:37Z
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 FUENTES-TRILLO, Azahara et al. Benchmarking different approaches for Norovirus genome assembly in metagenome samples. BMC Genomics, v. 22, 849, p. 1 - 12, 2021.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/50884
dc.identifier.issn.pt_BR.fl_str_mv 1471-2164
dc.identifier.doi.none.fl_str_mv 10.1186/s12864-021-08067-2
identifier_str_mv FUENTES-TRILLO, Azahara et al. Benchmarking different approaches for Norovirus genome assembly in metagenome samples. BMC Genomics, v. 22, 849, p. 1 - 12, 2021.
1471-2164
10.1186/s12864-021-08067-2
url https://www.arca.fiocruz.br/handle/icict/50884
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 BMC
publisher.none.fl_str_mv BMC
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)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/50884/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/50884/2/JulianaRS_Andrade_etal_IOC_2021.pdf
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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