Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes

BMC Research Notes

Table 3 Comparison of Arapan-S with ABySS, SSAKE, Velvet, QSRA, Minimus and Mira assemblers on four Benchmark Virus Genomes

Species	Assembler	Contigs ≥ 800 bp	Total length	Mean size (bp)	N50 (bp)	Largest contig (bp)	Genome coverage (%)
Bovine Respiratory Coronavirus AH187	Arapan-S	1	30937	30937	30937	30937	99.90
	ABySS	1	30924	30924.00	30924	30924	99.85
	SSAKE	9	27428	3047.56	3447	9868	88.57
	Velvet	3	30951	10317.00	25461	25461	99.94
	QSRA	8	29617	3702.125	-	11695	95.63
	Minimus	1	31026	31026	31026	31026	100.18
	Mira	8	28803	3600.37	3192	12305	93.51
Calf-giraffe Coronavirus US/OH3/2006	Arapan-S	1	30836	30836	30836	30836	99.53
	ABySS	2	30652	15326.00	18956	18956	98.94
	SSAKE	11	17005	1545.91	892	2683	54.89
	Velvet	3	30951	10317.00	25461	25461	99.91
	QSRA	2	2107	1053.5	-	1173	6.80
	Minimus	1	30979	30979	30979	30979	100.00
	Mira	5	33850	6770	20763	20763	109.28
Waterbuck Coronavirus US/OH-WD358-TC/1994	Arapan-S	1	30995	30995.00	30995	30995	100.00
	ABySS	1	30944	30944.00	30944	30944	99.86
	SSAKE	13	21780	1675.38	1063	5343	70.27
	Velvet	8	12505	1563.12	967	2162	40.34
	QSRA	5	4638	927.6	-	1174	14.96
	Minimus	1	30995	30995	30995	30995	100.00
	Mira	6	34011	5668.5	10510	10983	109.73
White-tailed Deer Coronavirus US/OH-WD470/1994	Arapan-S	1	31018	31018.00	31018	31018	99.99
	ABySS	2	30943	15471.50	21535	21535	99.75
	SSAKE	5	13925	2785.00	956	6100	44.89
	Velvet	10	17800	1780.00	1090	3430	57.38
	QSRA	8	7422	927.75	-	1323	23.93
	Minimus	1	31019	31019	31019	31019	100.00
	Mira	10	34892	3489.2	6174	9191	112.48

Only contigs whose lengths ≥ 800 were selected. When the assembler generated only one contig, the N50 value and the mean size are equal to the size of the corresponding contig. Genome coverage was calculated by dividing the total length by the genome length (EBI).

ISSN: 1756-0500