DOI: 10.1101/479105Nov 27, 2018Paper

Choice of assembly software has a critical impact on virome characterisation

BioRxiv : the Preprint Server for Biology
Thomas D S SuttonColin Hill

Abstract

Background: The viral component of microbial communities play 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 ...Continue Reading

Related Concepts

Antiviral Agents
Bacteriophages
Genome
Computer Software
Virus Cultivation
Virus
Fragmentation Procedure
Virus Assembly
Shapes
Downstream

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