Table 1. The number of core genes unrecalled at each depth comparing for different assemblers based on simulated data.
| Read length | Assemblers | Read depth | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10× | 20× | 30× | 40× | 50× | 60× | 70× | 80× | 90× | 100× | |||
| S. enterica (LT2) | 150 bp | SPAdes | 1404–1419 | 64–74 | 3–4a | 3–4 | 3 | 3–4 | 3–4 | 3 | 3–4 | 2–3 |
| (Size = 4.9 Mb) | CLC | 1680–1688 | 241–243 | 10–30 | 3–12 | 2 | 3 | 2–3 | 1–3 | 2–3 | 2–4 | |
| SKESA | 2382–2443 | 1125–1157 | 62–68 | 13–14 | 8–9 | 5 | 5 | 5 | 5 | 5 | ||
| 250 bp | SPAdes | 728–752 | 15–27 | 3–4 | 2 | 1–2 | 1–2 | 1–2 | 2–3 | 1–2 | 2–3 | |
| CLC | 964–1025 | 55–113 | 5 | 1–2 | 2–3 | 2–3 | 2 | 2 | 2–4 | 2–5 | ||
| SKESA | 1692–1697 | 169–175 | 12–17 | 3 | 2 | 2 | 2 | 2 | 2 | 2 | ||
| L. monocytogens | 150 bp | SPAdes | 1036 | 48 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| (IAI39) | CLC | 1223–1226 | 139–143 | 3–5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| (Size = 2.9 Mb) | SKESA | 1839 | 790–791 | 32 | 1 | 0–1 | 1 | 1 | 1 | 1 | 1 | |
| 250 bp | SPAdes | 531–560 | 12–21 | 0–1 | 0 | 0–1 | 0 | 0–1 | 0 | 0 | 0 | |
| CLC | 686–735 | 36–66 | 0–2 | 0 | 0–2 | 0 | 0 | 0 | 0 | 0 | ||
| SKESA | 1217–1267 | 111–126 | 3–11 | 1–3 | 1 | 1 | 1 | 1 | 1 | 0–1 | ||
| E. coli (EGD-e) | 150 bp | SPAdes | 1188 | 61 | 4 | 4 | 3–4 | 4 | 3–5 | 3 | 2–3 | 3–4 |
| (Size = 4.6 Mb) | CLC | 1411–1416 | 197–202 | 30–32 | 5–8 | 5–6 | 4–5 | 5 | 2–6 | 5 | 5–6 | |
| SKESA | 2089 | 989 | 54 | 14 | 9–11 | 8 | 8 | 7–8 | 7 | 7 | ||
| 250 bp | SPAdes | 611–629 | 21–22 | 4 | 3 | 2–3 | 3 | 3 | 2–3 | 2 | 2 | |
| CLC | 811-839 | 40–60 | 4–6 | 3–4 | 3–4 | 2–4 | 3–4 | 4–5 | 2 | 4 | ||
| SKESA | 1403–1432 | 132–135 | 13–14 | 7–8 | 7 | 6–7 | 6–7 | 6 | 6 | 6 | ||
Notes.
a
The gray fill represents the minimum read depth needed to achieve the stable number of core genes unrecalled for the combing of different read lengths and assemblers.