Next-generation sequencing for virus detection: covering all the bases.

ABSTRACT:

Background

The use of next-generation sequencing has become an established method for virus detection. Efficient study design for accurate detection relies on the optimal amount of data representing a significant portion of a virus genome.

Findings

In this study, genome coverage at different sequencing depths was determined for a number of viruses, viroids, hosts and sequencing library types, using both read-mapping and de novo assembly-based approaches. The results highlighted the strength of ribo-depleted RNA and sRNA in obtaining saturated genome coverage with the least amount of data, while even though the poly(A)-selected RNA yielded virus-derived reads, it was insufficient to cover the complete genome of a non-polyadenylated virus. The ribo-depleted RNA data also outpe

SUBMITTER: Visser M 

PROVIDER: S-EPMC4890495 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature