Fig. 1
From: Scalable long-read nanopore HPV16 amplicon-based whole-genome sequencing
A trio primer set for HPV16 whole-genome sequencing enrichment. a Schematic of the primer design for viral pre-sequencing enrichment. On top of the panel, the tiling-path primers are set: T1 (dark red), T2 (light green), and T3 (blue), along with the U1 (yellow) primer set, which is essential for amplifying the ligated region at the genome’s terminus. At the bottom of the panel is the near full-length primer set (gray). b Representation of HPV16 in its integrated extrachromosomal form as a multi-tandem repeat (upper) and episomal form (lower). c HPV16 long-read analysis pipeline. ONT reads were base-called with Guppy, aligned using Minimap2, and processed with SAMtools. Variants were called with Clair3. De Novo Assembly was executed using Canu, followed by sequence alignment and phylogenetic analysis in MEGA. d Representative depth-of-coverage plot showing sequencing read depth across the CaSki HPV16 genome relative to the reference for combined amplicons.
