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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.date.accessioned2019-06-11T15:46:43Z
dc.date.available2019-06-11T15:46:43Z
dc.date.issued2019-01-28
dc.identifier.citationSutton TDS, Clooney AG, Ryan FJ, Ross RP, Hill C. Choice of assembly software has a critical impact on virome characterisation. Microbiome 2019;7(1):12; doi http://dx.doi.org/10.1186/s40168-019-0626-5.en_US
dc.identifier.urihttp://hdl.handle.net/11019/1663
dc.descriptionpeer-revieweden_US
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_US
dc.language.isoenen_US
dc.publisherBiomed Centralen_US
dc.relation.ispartofseriesMicrobiome;vol 7
dc.subjectViromeen_US
dc.subjectViralen_US
dc.subjectAssemblyen_US
dc.subjectMetagenomeen_US
dc.subjectBenchmarkingen_US
dc.subjectComparisonen_US
dc.subjectBacteriophageen_US
dc.subjectPhageen_US
dc.titleChoice of assembly software has a critical impact on virome characterisationen_US
dc.typeArticleen_US
dc.date.updated2019-02-03T04:18:13Z
dc.language.rfc3066en
dc.rights.holderThe Author(s).
dc.identifier.doihttps://doi.org/10.1186/s40168-019-0626-5
dc.contributor.sponsorScience Foundation Irelanden_US
dc.contributor.sponsorEuropean Regional Development Funden_US
dc.contributor.sponsorJanssen Biotech, Inc.en_US
dc.contributor.sponsorGrantNumberSFI/12/RC/2273en_US
dc.contributor.sponsorGrantNumberSFI/14/SP APC/B3032en_US
refterms.dateFOA2019-06-11T15:46:43Z


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