TABLE 1.
Homology-based iterative assembly.
| Iterations/strain | IndV1/PakV1 | IndV2/PakV2 | IndV3/PakV3 | IndV4qm using HiC/PakV4 | STE2/SDA-500 (Waterhouse et al., 2020) | IndV3s/PakV3s stitched |
| Longest scaffold (Mb) | 5.9/3.4 | 21.3/9.8 | 24.3/17.1 | 47.5/48.9 | 10.2/7 | 58/62.5 |
| L50 | 37/85 | 11/22 | 9/12 | 3/4 | 16/38 | 2/2 |
| N50* (Mb) | 1.7/0.8 | 5.09/3.18 | 6.5/6.9 | 39.3/18.9 | 4.19/1.7 | 43/51.4 |
| Number of scaffolds | 7806/1110 | 7661/770 | 7657/742 | 7423/638 | 7677/873 | 5/5 |
| Assembly size (Mb) | 210/225 | 213/230 | 213/244 | 220/244.4 | 210/225 | 180/193.5 |
| Percent Ns | 5.62/12.95 | 6.9/14.88 | 6.91/19.71 | 7.14/19.73 | 5.6/12.9 | 6.44/16.93 |
Assembly metrics for Indian (STE2) and Pakistani (SDA-500) strains after every iteration. *N50 is the scaffold length, x, such that 50% of the genome is assembled on scaffolds of length x or longer.