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).