Figure 7

Bioinformatics pipeline used for the long-read only assembly of the Ducapox genome. Basecalling of reads was performed using Guppy v4.0.11. Adapter sequences in reads were removed using Porechop v.0.2.4. Reads were subsequently filtered to a minimum length of 3000 bases using Nanofilt v2.6.0. An initial assembly was performed using Flye v.2.8 (using reads containing both viral and non-viral DNA sequences), after which a BLAST search for each contig generated was performed against the NCBI nucleotide database. A file containing all non-viral reads was used to generate an exclusive viral read set by mapping reads to the non-viral contigs using Minimap2 v 2.17-r941, followed by extraction of the unmapped reads using Samtools v1.7. A Flye assembly was performed on the exclusive viral reads set, which was subsequently polished with TandemTools, followed by 3 rounds of Racon v.1.4.13 polishing, and a final polishing round using Medaka v0.11.5 to generate a 159,696 bp genome. An incorrect insertion within an adenine homopolymer region of this assembly was corrected, producing a final genome sequence length of 159,695 bp.