2.7. Genome Assembly and Viral Genome Detection

Cleaned sequence reads were assembled using MEGAHIT assembler (v1.2.9) [30] with default parameters. QUAST (v5.0.2) [31] was used to assess the quality and quantity of assembled genomic contigs with default parameters. Potential viral contigs were then predicted using VirSorter (v1.0.3) [32] and VirFinder (v1.1) [33]. In this study, those putative viruses and proviruses sorted and classified into VirSorter categories 1 to 6 (including all predicted viruses and prophages) and those run through VirFinder under appropriate sorting conditions (score ≥ 0.7 and p < 0.05) were considered viral [5]. To access the completeness and qualities of sorted viral contigs, CheckV (v0.7.0) was used in end-to-end mode with default parameters [34].