Choice of assembly software has a critical impact on virome characterisation

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dc.contributor.author Sutton, Thomas D. S.
dc.contributor.author Clooney, Adam G.
dc.contributor.author Ryan, Feargal J.
dc.contributor.author Ross, R. Paul
dc.contributor.author Hill, Colin
dc.date.accessioned 2019-11-25T20:29:00Z
dc.date.available 2019-11-25T20:29:00Z
dc.date.issued 2019-01-28
dc.identifier.citation Sutton, 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/s40168-019-0626-5 en
dc.identifier.volume 7 en
dc.identifier.issued 1 en
dc.identifier.startpage 1 en
dc.identifier.endpage 15 en
dc.identifier.uri http://hdl.handle.net/10468/9221
dc.identifier.doi 10.1186/s40168-019-0626-5 en
dc.description.abstract Background: 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.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher BioMed Central Ltd. en
dc.relation.uri https://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.uri https://creativecommons.org/licenses/by/4.0/ en
dc.subject Virome en
dc.subject Viral en
dc.subject Assembly en
dc.subject Metagenome en
dc.subject Benchmark en
dc.subject Comparison en
dc.subject Bacteriophage en
dc.subject Phage en
dc.title Choice of assembly software has a critical impact on virome characterisation en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Colin Hill, School of Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: c.hill@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Janssen Biotech en
dc.contributor.funder Science Foundation Ireland en
dc.contributor.funder European Regional Development Fund en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Microbiome en
dc.internal.IRISemailaddress c.hill@ucc.ie en
dc.identifier.articleid 12 en
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/ en
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Spokes Programme/14/SP APC/B3032/IE/Gut Phageomics - Phage as diagnostics and/or therapeutics in IBD/ en
dc.identifier.eissn 2049-2618


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© 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. Except where otherwise noted, this item's license is described as © 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.
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