Supplementary file 2 contains information about all default settings and versions used for each software tool.

Metaflye_v : metaFlye build 2.9-b1774, (git revision af269a3470db78c9c95934e1a5aa5ce218640804 ) with --scaffold option 

For the viralTools pipeline we used the latest versions of the following software tools available in conda:  
Minimap2: 2.22-r1101
Prodigal: V2.6.3
viralVerify 1.1
Samtools& bcftools 1.13
Seqtk 1.3-r106
Minced 0.4.2
Freebayes v0.9.21
CD-HIT-EST v.4.8.1, similarity threshold 0.95
CheckV v0.7.0
Blastn, v. 2.6.0+, max evalue 1E-5, min identity 0.9,  task = blastn-short 

All these tools were run with their default settings unless otherwise specified