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    Choice of assembly software has a critical impact on virome characterisation

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    Author
    Sutton, Thomas D S
    Clooney, Adam G
    Ryan, Feargal J
    Ross, R Paul
    Hill, Colin
    Keyword
    Virome
    Viral
    Assembly
    Metagenome
    Benchmarking
    Comparison
    Bacteriophage
    Phage
    Date
    2019-01-28
    
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    URI
    http://hdl.handle.net/11019/1663
    Citation
    Sutton 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.
    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.
    Funder
    Science Foundation Ireland; European Regional Development Fund; Janssen Biotech, Inc.
    Grant Number
    SFI/12/RC/2273; SFI/14/SP APC/B3032
    ae974a485f413a2113503eed53cd6c53
    https://doi.org/10.1186/s40168-019-0626-5
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    Teagasc publications in Biomed Central

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