454 sequencing system software

The P. yeei CCUG 32053 genome was sequenced by combining the Oxford Nanopore and Illumina technologies. Whole genome sequencing was performed using a MinION instrument with a R9.4 flow cell and 1D ligation kit SQK-LSK108, and an Illumina MiSeq instrument with 2×300 paired-end mode and v3 MiSeq chemistry kit, which produced 77,644 (257 Mb) and 1,639,864 (488.5 Mb) reads, respectively. Raw MinION data base calling was performed using Albacore v2.0.2 (Oxford Nanopore Technologies). Adaptors were removed using Porechop v.0.2.1¹. Genome assembly was carried out using Canu v1.6 (Koren et al., 2017 (link)) and subsequently polished with Racon v0.5.0 (Vaser et al., 2017 (link)). Illumina reads were then mapped against the acquired genome using bwa v0.7.15-r1142-dirty (Li and Durbin, 2010 (link)) and final sequence correction was performed using Pilon v1.21 (Walker et al., 2014 (link)). The genome assembly was verified by comparison with assemblies obtained using Newbler De Novo Assembler v3.0 (454 Sequencing System Software, Roche) and SPAdes v3.11.1 (Bankevich et al., 2012 (link)).

Raw reads were quality trimmed and assembled de novo using the 454 Sequencing System Software (v. 2.8; Roche, Mannheim, Germany), and the resulting contigs were arranged in order to match the CPXV genome. Draft CPXV genomes were further confirmed by reference guided mapping (454 Sequencing System Software) using the “–rst 0” parameter with respect to their repetitive genomic termini. The mean genomic coverage of each full-length CPXV sequence exceeded the minimal acceptable coverage of 20. Full-length CPXV sequences were annotated analogue to the nomenclature of the CPXV Brighton Red reference strain (AF482758) as described elsewhere [27 (link)].