Table 2.

Relative strengths of five pangenome graph construction tools. Explanation of rows: (1) efficacy of construction algorithm, measuring wall-clock time; (2) degree to which variants (e.g., SNPs) are retained; (3) ability of a tool to perform well on large datasets, both in comparison to other tools but also compared to smaller datasets; (4) ability to modify the produced data structure to add or remove haplotypes; (5) property of producing the same result irrespective of perturbations, such as permutation of the input order, and repeating the same run; (6) existence of tools (and operations) that can be applied to the resulting graphs; (7) whether input haplotypes information is retained by the tools, and if so, its space efficiency; (8) whether the entire graph can be directly visualized and interpreted; (9) easiness of “zooming in” a specific genomic region and interpret variants; (10) summarizes the functionalities provided by the tools to annotate the pangenomes with genomic data; (11) ability to share information between the graph and a linear reference

Metric	Bifrost	pggb	Minigraph-Cactus	Minigraph	mdbg
1) Construction speed	$\bullet \bullet \circ$	$\bullet \circ \circ$	$\bullet \circ \circ$	$\bullet \bullet \circ$	$\bullet \bullet \bullet$
2) Variations	$\bullet \bullet \bullet$	$\bullet \bullet \bullet$	$\bullet \bullet \bullet$	$\bullet \bullet \circ$	$\bullet \bullet \circ$
3) Scalablilty	$\bullet \bullet \bullet$	$\bullet \circ \circ$	$\bullet \circ \circ$	$\bullet \bullet \circ$	$\bullet \bullet \bullet$
4) Editability	$\bullet \bullet \bullet$	$\bullet \bullet \circ$	$\bullet \circ \circ$	$\bullet \bullet \circ$	$\bullet \circ \circ$
5) Stability	$\bullet \bullet \bullet$	$\bullet \circ \circ$	$\bullet \circ \circ$	$\bullet \bullet \circ$	$\bullet \bullet \bullet$
6) Accessibility by downstream applications	$\bullet \circ \circ$	$\bullet \bullet \bullet$	$\bullet \bullet \bullet$	$\bullet \bullet \circ$	$\bullet \circ \circ$
7) Haplotype compression performance	$\bullet \bullet \circ$	$\bullet \bullet \bullet$	$\bullet \bullet \bullet$	$\bullet \circ \circ$	$\bullet \circ \circ$
8) Ease of visualization	$\bullet \circ \circ$	$\bullet \bullet \circ$	$\bullet \bullet \circ$	$\bullet \bullet \bullet$	$\bullet \bullet \bullet$
9) Loci visualization and interpretability	$\bullet \circ \circ$	$\bullet \bullet \circ$	$\bullet \bullet \bullet$	$\bullet \bullet \circ$	$\bullet \circ \circ$
10) Metadata and annotation	$\bullet \bullet \circ$	$\bullet \bullet \bullet$	$\bullet \bullet \circ$	$\bullet \circ \circ$	$\bullet \circ \circ$
11) Compatibility with a linear reference coordinates	$\bullet \circ \circ$	$\bullet \bullet \bullet$	$\bullet \bullet \bullet$	$\bullet \bullet \circ$	$\bullet \circ \circ$