Table 4 Minimal sequencing depth to achieve an assembly with a similar quality to assemblies obtained with depth ≥ 100X data under the same strategy and assembler.

Model	Assembly parameters	Short-reads only		Long-reads only		Hybrid
Model	Assembly parameters	Megahit	Unicycler	Canu	Unicycler	Wengan	Unicycler
B. henselae	Depth for short-reads	25X	25X	-	–	200X*	25X
B. henselae	Depth for long-reads	–	–	25X	25X	100X*	25X
E. coli	Depth for short-reads	12.5X	12.5X	-	–	50X	12.5X
E. coli	Depth for long-reads	–	–	25X	25X	25X	12.5X
P. aeruginosa	Depth for short-reads	25X	25X	-	–	400X**	25X
P. aeruginosa	Depth for long-reads	–		25X	25X	25X	12.5X
X. fastidiosa	Depth for short-reads	12.5X	12.5X	–	–	50X	12.5X
X. fastidiosa	Depth for long-reads	–	–	12.5X	12.5X	12.5X	6.5X

* Genome assembly was only achieved using this minimal value (i.e. no genome sequence was obtained using lower depths).
** Genome assembly was achieved with lower depths but with a reduced quality.

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