Nanopore sequencing is a credible alternative to recover complete genomes of geminiviruses

Within the context of CRESS DNA viruses studies, we implemented two alternative long-read NGS protocols, one that is agnostic to the sequence (without a priori) and the other that use specific primers to target a virus (with a priori). Agnostic and specific long read NGS-based assembled genomes of two capulavirus strains (TrV1-B and TrV1-C) were compared to those obtained using the gold standard technique of Sanger sequencing. Both protocols allowed the detection and accurate full genome characterization of both strains. Globally, the assembled genomes were very similar (99.5-99.7% identity) to the Sanger sequences consensus.