Choice of assembly software has a critical impact on virome characterisation

Sutton, Thomas D. S.; Clooney, Adam G.; Ryan, Feargal J.; Ross, R. Paul; Hill, Colin

Choice of assembly software has a critical impact on virome characterisation

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.contributor.funder	Janssen Biotech	en
dc.contributor.funder	Science Foundation Ireland	en
dc.contributor.funder	European Regional Development Fund	en
dc.date.accessioned	2019-11-25T20:29:00Z
dc.date.available	2019-11-25T20:29:00Z
dc.date.issued	2019-01-28
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.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	12	en
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.doi	10.1186/s40168-019-0626-5	en
dc.identifier.eissn	2049-2618
dc.identifier.endpage	15	en
dc.identifier.issued	1	en
dc.identifier.journaltitle	Microbiome	en
dc.identifier.startpage	1	en
dc.identifier.uri	https://hdl.handle.net/10468/9221
dc.identifier.volume	7	en
dc.language.iso	en	en
dc.publisher	BioMed Central Ltd.	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.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