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

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

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

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)

ISSN: 2049-2618