Table 3.

Comparison between space-efficient colored de Bruijn graph construction methods for 4000, 8000 and 16 000 Salmonella strains using $\text{VariMerge}$ versus competing methods

Dataset	No. of k-mers (Billion)	Program	Output size (GB)	Time	RAM (GB)
4000	1.1	$\text{Vari}$/Rainbowfish	51	10 h 25 min	136
		Bloom Filter Trie	99	51 h 42 min	120
		Multi-BRWT	1.3 TB	42 h 23 min	156
		Mantis/Method of Almodaresi et al.	36	5 h 58 min	313
		$\text{VariMerge}$	51	10 h 25 min	136
8000	2.4	$\text{Vari}$/Rainbowfish	114	37 h 27 min	271
		Bloom Filter Trie	N/A	N/A	N/A
		Multi-BRWT	N/A	N/A	N/A
		Mantis/Method of Almodaresi et al.	38	13 h 37 min	370
		$\text{VariMerge}$	106	26 h 30 min	137
16 000	5.8	$\text{Vari}$/Rainbowfish	N/A	N/A	N/A
		Bloom Filter Trie	N/A	N/A	N/A
		Multi-BRWT	N/A	N/A	N/A
		Mantis/method of Almodaresi et al.	256	36 h 12 min	316
		$\text{VariMerge}$	233	69 h 8 min	254

Note: We report N/A for any method that exceeded 140 CPU hours, 4 TB of disk space and 750 GB of memory. We anticipate add-on methods to compress better but will still consume the resources shown for their base method because they reuse base the method’s output. We measured RAM as max resident set size. Mantis authors noted their use of memory mapped I/O means this reveals opportunistic consumption and not necessarily requirement for their program. To the best of our knowledge, no extra external memory is needed for Bloom Filter Trie, Multi-BRWT, Mantis and the method of Almodaresi et al., so it is omitted from the table.