Latest Publications
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies
Ryan Cook, Nathan Brown, Branko Rihtman, Slawomir Michniewski, Tamsin Redgwell, Martha Clokie, Dov J. Stekel, Yin Chen, David J. Scanlan, Jon L. Hobman, Andrew Nelson, Michael A. Jones, Darren Smith and Andrew Millard
ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community. Thus, we constructed a mock bacteriophage community of previously sequenced phage genomes and sequenced them using Illumina, Nanopore and PacBio sequencing technologies and tested a number of different assembly approaches. Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies. When using a single technology, Illumina only was the best approach. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.