Fig. 1 End-to-end workflow for obtaining complete viral genome sequences without assembly
The inherent genetic complexity of virus populations poses technical difficulties for recovering complete virus genomes from the environment. To address these challenges, we developed an assembly-free, single-molecule nanopore sequencing approach enabling direct recovery of complete viral genome sequences from environmental samples. Water was collected at three different depths from the Pacific Ocean near Hawaii and viral particles were enriched from each sample (Fig. 1a). A library was prepared from each sample and sequenced, generating tens of thousands of sequences (Fig. 1b) all containing the hallmark of complete dsDNA tailed bacteriophage: direct terminal repeats (DTRs). We designed a custom assembly-free bioinformatic pipeline to cluster and polish these reads to produce novel viral genomes (Fig. 1c).