Viral contigs of Virome Benchmark

The VLP sequencing data were then assembled using the selected assemblers. Default parameters were used unless otherwise stated. Briefly, for the NGS data, we used IDBA-UD (v1.1.4), MEGAHIT (v1.2.9), and metaSPAdes (v3.15.4). For the TGS data, we selected Canu (v2.2), FALCON (v1.8.1), Hifiasm-meta (v0.3), metaFlye (v2.9.1), and wtdbg2 (v2.5). For hybrid assembly that combines the NGS and TGS data, we used IDBA-hyb (v1.1.3), hybridSPAdes (v3.15.4), metaViralSPAdes (v3.15.4) and OPERA-MS (v0.83).
Dereplication was performed on contigs obtained by each tool on each sample or multi-tools on all samples using cd-hit (v4.6.8) with a parameter of -c 0.99 according to a previous study. Viral contigs were then identified using a similar procedure to human Gut Virome Database (GVD), with modifications. Briefly, the following virus recognition software were firstly used, including VirSorter2 (v2.2.4), DeepVirFinder (v1.0), VirFinder (v1.1), Seeker, and PPR-Meta (v1.1) . Their parameters were listed as the following. 1. VirSorter score ≥ 0.7, 2. DeepVirFinder pvalue<0.05, 3. VirFinder score > 0.6, 4. Seeker with the default parameter, 5. PPR-Meta phage score > 0.7. Secondly, a contig was considered as a virus if it passed at least two out the above five criteria and had sequence length >1.5kb.