Choice of assembly software has a critical impact on virome characterisation

dc.contributor.authorSutton, Thomas D. S.
dc.contributor.authorClooney, Adam G.
dc.contributor.authorRyan, Feargal J.
dc.contributor.authorRoss, R. Paul
dc.contributor.authorHill, Colin
dc.contributor.funderJanssen Biotechen
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderEuropean Regional Development Funden
dc.date.accessioned2019-11-25T20:29:00Z
dc.date.available2019-11-25T20:29:00Z
dc.date.issued2019-01-28
dc.description.abstractBackground: The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets. Design: This study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely, simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes. Results: Assembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low-accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid12en
dc.identifier.citationSutton, T.D., Clooney, A.G., Ryan, F.J., Ross, R.P. and Hill, C. (2019). Choice of assembly software has a critical impact on virome characterisation. Microbiome, 7(1), 12. (15pp) doi:10.1186/s40168-019-0626-5en
dc.identifier.doi10.1186/s40168-019-0626-5en
dc.identifier.eissn2049-2618
dc.identifier.endpage15en
dc.identifier.issued1en
dc.identifier.journaltitleMicrobiomeen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/9221
dc.identifier.volume7en
dc.language.isoenen
dc.publisherBioMed Central Ltd.en
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Spokes Programme/14/SP APC/B3032/IE/Gut Phageomics - Phage as diagnostics and/or therapeutics in IBD/en
dc.relation.urihttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0626-5
dc.rights© The Author(s). 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectViromeen
dc.subjectViralen
dc.subjectAssemblyen
dc.subjectMetagenomeen
dc.subjectBenchmarken
dc.subjectComparisonen
dc.subjectBacteriophageen
dc.subjectPhageen
dc.titleChoice of assembly software has a critical impact on virome characterisationen
dc.typeArticle (peer-reviewed)en
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