Evaluation of viral genome assembly and diversity estimation in deep metagenomes

[Background] Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing pl...

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Detalles Bibliográficos
Autores: Aguirre de Cárcer, Daniel, Angly, Florent, Alcamí, Antonio
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2014
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/124422
Acceso en línea:http://hdl.handle.net/10261/124422
Access Level:acceso abierto
Palabra clave:Assembly
Diversity
Metagenomics
Virome
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spelling Evaluation of viral genome assembly and diversity estimation in deep metagenomesAguirre de Cárcer, DanielAngly, FlorentAlcamí, AntonioAssemblyDiversityMetagenomicsVirome[Background] Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing platforms and assemblers. Further, it investigates the suitability of different methods to estimate viral diversity in metagenomes.[Results] We created in silico metagenomes mimicking various platforms at different sequencing depths. The CLC assembler revealed subpar compared to IDBA_UD and CAMERA, which are metagenomic-specific. Up to a saturation point, Illumina platforms proved more capable of reconstructing large portions of viral genomes compared to 454. Read length was an important factor for limiting chimericity, while scaffolding marginally improved contig length and accuracy. The genome length of the various viruses in the metagenomes did not significantly affect genome reconstruction, but the co-existence of highly similar genomes was detrimental. When evaluating diversity estimation tools, we found that PHACCS results were more accurate than those from CatchAll and clustering, which were both orders of magnitude above expected.[Conclusions] Assemblers designed specifically for the analysis of metagenomes should be used to facilitate the creation of high-quality long contigs. Despite the high coverage possible, scientists should not expect to always obtain complete genomes, because their reconstruction may be hindered by co-existing species bearing highly similar genomic regions. Further development of metagenomics-oriented assemblers may help bypass these limitations in future studies. Meanwhile, the lack of fully reconstructed communities keeps methods to estimate viral diversity relevant. While none of the three methods tested had absolute precision, only PHACCS was deemed suitable for comparative studies. © 2015 Aguirre de Cárcer et al.. licensee BioMed Central Ltd.This work was funded in part by the Spanish Ministry of Science and Innovation grant CTM2011-15091-E/ANT. Daniel Aguirre de Cárcer was supported by the Marie Curie International Incoming Fellow grant PIIF-GA- 2012-328287. Florent Angly was supported by the Australian Research Council’s Discovery Early Career Research Award DE120101213We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI)Peer ReviewedBioMed CentralMinisterio de Ciencia e Innovación (España)Australian Research CouncilCSIC - Unidad de Recursos de Información Científica para la Investigación (URICI)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2015201520142015info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/124422reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1186/1471-2164-15-989Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1244222026-05-22T06:33:51Z
dc.title.none.fl_str_mv Evaluation of viral genome assembly and diversity estimation in deep metagenomes
title Evaluation of viral genome assembly and diversity estimation in deep metagenomes
spellingShingle Evaluation of viral genome assembly and diversity estimation in deep metagenomes
Aguirre de Cárcer, Daniel
Assembly
Diversity
Metagenomics
Virome
title_short Evaluation of viral genome assembly and diversity estimation in deep metagenomes
title_full Evaluation of viral genome assembly and diversity estimation in deep metagenomes
title_fullStr Evaluation of viral genome assembly and diversity estimation in deep metagenomes
title_full_unstemmed Evaluation of viral genome assembly and diversity estimation in deep metagenomes
title_sort Evaluation of viral genome assembly and diversity estimation in deep metagenomes
dc.creator.none.fl_str_mv Aguirre de Cárcer, Daniel
Angly, Florent
Alcamí, Antonio
author Aguirre de Cárcer, Daniel
author_facet Aguirre de Cárcer, Daniel
Angly, Florent
Alcamí, Antonio
author_role author
author2 Angly, Florent
Alcamí, Antonio
author2_role author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
Australian Research Council
CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Assembly
Diversity
Metagenomics
Virome
topic Assembly
Diversity
Metagenomics
Virome
description [Background] Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing platforms and assemblers. Further, it investigates the suitability of different methods to estimate viral diversity in metagenomes.
publishDate 2014
dc.date.none.fl_str_mv 2014
2015
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/124422
url http://hdl.handle.net/10261/124422
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1186/1471-2164-15-989
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.812429

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