Table 1.

Computational performance of each tool

	Index			Map and genotype
	Disk (Mb)	Max RAM (Mb)	Speed (sec)	Max RAM (Mb)	Speed (reads/sec)
vg	29	609	105	605[158]	3,961
gramtools	153	480	32	632	34,290
GraphTyper2	–	–	–	869[88]	7,604

Index: genome graph processing step allowing subsequent read mapping. For vg, includes a graph pruning step to reduce graph complexity (else temporary disk use exceeded 500 Gb before completion, see “vg and GraphtTyper2 genome graph construction” section). GraphTyper2 has no separate indexing operation. Map and Genotype: Speed shows the average number of reads mapped across the 17 samples (10.7 million) divided by the average CPU time. vg and GraphTyper2 have separate read mapping and genotyping steps: for speed, CPU time is summed, and for RAM, mapping is shown followed by genotyping in square brackets. GraphTyper2 does not implement its own mapping but requires an input file of reads mapped to a linear reference genome; mapping RAM and speed is shown for bowtie2 with default parameters. metrics: Mb, megabytes; sec, total CPU seconds (accounts for multi-threading, 10 threads used for genotyping in each tool)