Table 2. The number of core-gene differences between assembly and the reference genome in each depth comparing for different assemblers based on real sequenced data.

	Read length	Assemblers	Read depth
			10×	20×	30×	40×	50×	60×	70×	80×	90×	100×
S. enterica	150 bp	SPAdes	180–206	8–11	7–8a	7–8	7–8	7–8	7–8	7–7	6–8	7–8
	(CP023508.1)	CLC	384–439	13–17	7–8	7–8	7–9	7–9	7–7	7–9	7–9	7–7
	SRR5866640	SKESA	2669–2864	871–1177	89–652	24–55	13–14	12–13	13–14	13	13–14	13
	250 bp	SPAdes	185–214	11–15	8–9	8–10	8–9	8–9	8	8–9	8–9	8
	(CP036165.1)	CLC	338–392	12–28	10	7–11	7–8	5–9	8–9	5–8	8–9	7–8
	SRR6929558	SKESA	2373–2570	874–885	120–145	16–22	11–12	10–11	10	10	10–11	10
L. monocytogens	150 bp	SPAdes	376–423	12–14	0–1	0	0	0	0	0	0	0
	(CP013919.1)	CLC	593–658	41–60	3–5	0–2	0–1	1	0–1	1	1	0–1
	SRR3089759	SKESA	2000–2059	1144–1192	660–671	55–130	6–14	2–3	1–3	1–2	1	1
	250 bp	SPAdes	176–200	7–14	1–2	0–2	0	0	0–1	0	0	0
	(CP025565.1)	CLC	325–349	40–55	7–12	3–8	0–1	0–3	1	0–1	0	0
	SRR6347431	SKESA	1521–1620	597–612	101–125	22–39	6–7	3–5	1–3	0–2	0–3	1–2
E. coli	150 bp	SPAdes	97–122	11–12	9–12	9–10	10	9–11	9–10	9–10	9	9–10
	(CP029239.1)	CLC	217–234	21–26	12–17	11–14	11–13	11–13	11	11–12	11	11–13
	SRR6924239	SKESA	2017–2137	905–922	468–518	34–60	17–21	12–14	13	11–12	12	12
	250 bp	SPAdes	37–56	4	4	4	4	4	4	4	4	4
	(CP034799.1)	CLC	76–99	6	5–6	5–6	5–6	4–6	5–6	5–6	5–7	6–7
	SRR3205757	SKESA	1651–1780	449-553	22–30	7–8	6	6	6	6	6	6

Notes.

^aThe 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.