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

From: Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small 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
  1. 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).