Challenges in the analysis of viral metagenomes

Rose, Rebecca; Constantinides, Bede; Tapinos, Avraam; Robertson, David L; Prosperi, Mattia

Although metagenome assemblers generally outperform single genome assemblers in reconstructing different genomes simultaneously, the complexity of this task stipulates their tendency to collapse variation at or beneath strain level into consensus sequences. Even to this end, their effectiveness may be limited as a consequence of extreme variation within specific RNA virus populations due to mutation and recombination, and low and/or uneven sequencing coverage across a particular genome. Furthermore, it should be noted that de novo assembly is particularly sensitive to the quality of input sequences, meaning that problems during sample extraction, enrichment and library preparation can be highly detrimental to downstream analyses. Of key importance therefore are quality control methods for detecting, and where appropriate correcting, problems associated with contamination (Darling et al. 2014; Orton et al. 2015) , primer read-through and low quality reads (reviewed in Leggett et al. 2013 ).