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Table 1 Virus recovery of VIBRANT, VirFinder, and VirSorter from mixed metagenomes and a virome

From: VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

Metagenome Seqs. total (≥ 1 kb) Seqs. ≥ 4 ORFs Metric VIBRANT VirFinder (score ≥ 0.90) VIBRANT vs. VirFinder VirSorter(cat. 1 and 2) VIBRANT vs. VirSorter
Human gut: adenoma 34,883 11,360 Total putative viruses 527 604 0.87 284 1.86
Total virus length (bp) c5,234,242 1,696,118 3.09 3,982,292 1.31
Total virus proteins 7,661 2,134 3.59 5,484 1.40
Human gut: carcinoma 53,946 18,669 Total putative viruses 784 1,329 0.59 450 1.74
Total virus length (bp) 5,611,953 3,500,838 1.60 4,182,862 1.34
Total virus proteins 8,401 4,644 1.81 5,945 1.41
Human gut: healthy 42,739 17,079 Total putative viruses 565 672 0.84 309 1.83
Total virus length (bp) 5,623,082 2,411,049 2.33 4,512,571 1.25
Total virus proteins 8,202 3,230 2.54 6,127 1.34
Thermophilic compost 68,815 21,620 Total putative viruses 1,047 878 1.19 383 2.73
Total virus length (bp) 10,253,162 2,238,129 4.58 3,290,654 3.12
Total virus proteins 9,912 2,806 3.53 4,400 2.25
Freshwater lake (bog) 79,862 26,832 Total putative viruses 5,626 7,567 0.74 1,503 3.74
Total virus length (bp) 34,976,570 25,357,664 1.38 15,436,797 2.27
Total virus proteins 56,120 37,537 1.50 21,280 2.64
*Estuary virome 5,247 3,277 Total putative viruses 3,141 2,294 1.37 1,121 2.80
Total virus length (bp) 6,591,285 6,478,804 1.02 5,163,674 1.28
Total virus proteins 20,500 12,035 1.70 9,645 2.13
  1. Mixed community assembled metagenomes from human gut, thermophilic compost, and freshwater, as well as an estuary virome, were used to compare virus prediction ability between the three programs. For each assembly, the scaffolds were limited to a minimum length of 1000 bp. Only a subset of each dataset contained scaffolds encoding at least four open reading frames. VIBRANT, VirFinder (score minimum of 0.90), and VirSorter (categories 1 and 2) were compared by total viral predictions, total combined length of predicted viruses, and total combined proteins of predicted viruses. Comparison columns, denoted “VIBRANT vs. VirFinder” and “VIBRANT vs. VirSorter”, display the comparison ratio of the given metric; bold indicates greater performance by VIBRANT. The asterisk represents that VIBRANT, VirFinder and VirSorter were ran with alternate settings (see Methods)