Graph construction method impacts variation representation and analyses in a bovine super-pangenome

Table 1 Profiles of three bovine pangenomes constructed from autosomal sequences of twelve assemblies. Path steps are the total number of steps needed to trace all 12 assemblies through the graph

Parameter	Unit	minigraph	cactus	pggb
Nodes	N	427,012	198,431,246	179,575,371
Edges	N	606,926	272,102,708	245,150,846
Node length	bp	2,598,811,581	3,041,026,095	3,012,039,323
Path steps	N	3,358,976	1,621,936,527	1,442,793,659
Repetitive sequence	bp	1,107,501,421	1,361,489,638	1,415,552,890
Centromeric sequence	bp	2,939,789	291,982,193	255,091,362
CPU time	h	14^a	226^b	3,559
Max memory	GiB	7	54	46
GFA file size	GB	2.6	26.1	23.7

^aMinigraph required an additional 18 CPU hours to add P-lines
^bCactus uses soft masked assemblies as input, which required an additional 1571 CPU hours

ISSN: 1474-760X