Table 2.

Breakdown of the peak memory, peak disk and time required by $\text{VariMerge}$ to build the colored de Bruijn graph for 16 000 strains of Salmonella

	Input stats		de Bruijn graph			Color matrix			Combined requirements
Program and dataset	k-mers (B)	Colors	RAM (GB)	Time	Size (GB)	RAM (GB)	Time	Size (GB)	RAM (GB)	External memory (TB)	Time	Size (GB)
$\text{Vari}$(4C)	1.7 B	4000	135	10 h 53 min	0.46	53	2 h 34 min	51.8	135	1.6	13 h 27 min	52
$\text{Vari}$(4D)	2.4 B	4000	137	14 h 35 min	0.67	59	3 h 37 min	57.9	137	2.34	18 h 12 min	59
$\text{Merge}$(4C, 4D)	3.8 B	8000	17	2 h 59 min	1.00	118	57 min	107	118	0	3 h 56 min	108
$\text{Merge}$(8AB, 8CD)	5.8 B	16 000	25	4 h 53 min	1.60	254	2 h 10 min	232	254	0	7 h 3 min	233
$\text{VariMerge}$	5.8 B	16 000	137	54 h 47 min	1.60	254	14 h 21 min	232	254	2.34	69 h 8 min	233

Note: We note $\text{VariMerge}$ includes the resources required of the two 4000 runs of $\text{Vari}$ (i.e. $\text{Vari}$(4A) and $\text{Vari}$(4B)) and the merge run (i.e. $\text{Merge}$(4A, 4B)) from Table 1. No extra external memory is needed for merging so ‘0’ is in the external memory column for $\text{Merge}$.