Table 1.

Comparison of pan-genome tools. We analyzed tools for pan-genome analysis that are available or currently under development. This table lists the corresponding publications or websites. We compared the intended use cases of the tools and the prerequisite data required in order to use them. We evaluated the availability of features needed to work with the pan-genome in subsequent analyses, e.g. updating the set of included genomes. Furthermore, we assessed whether the proposed data structures take into account structural variants and whether it is possible to visualize the resulting pan-genome

Name	Objective	Input	Visualization	Structural	Functionality
			of pan-genome	Variants	Update		Possibility to
					Add	Remove	include annotation
svaha [9]	Graph construction	Reference sequence + variants	External	Yes	No	No	No
cdbg [2]	Graph construction	Multiple reference sequences	External	Yes	No	No	No
cdbg_search [6]	Graph construction	Multiple reference sequences	External	Yes	No	No	No
SplitMEM [44]	Graph construction	Multiple reference sequences	External	Yes	No	No	No
TwoPaCo [7]	Graph construction	Multiple reference sequences	External	Yes	No	No	No
GCSA2 [8]	Graph indexing	Variation graph	No	No	No	No	No
GCSA [10]	Graph indexing	Reference sequence + variants	No	No	No	No	No
	Multiple sequence mapping
BWBBLE [11]	Multiple sequence mapping	Reference sequence + variants	No	No	No	No	No
GenomeMapper [12]	Multiple sequence mapping	Reference sequence + variants	No	No	No	No	No
panVC [14]	Multiple sequence variant detection	Whole genome alignment	External	Yes	No	No	Yes
MHC-PRG [13]	Multiple sequence variant detection	Multiple sequence alignment	No	No	Yes	No	No
	Pan-genome data structure	AND variants
GenomeRing [3]	Pan-genome data structure	Whole genome alignment	Yes	Yes	No	No	Yes
JST [15]	Pan-genome data structure	Reference sequence + variants	No	Yes	Yes	Yes	Yes
vg [17]	Pan-genome data structure	Reference sequence + variants	External	Yes	Yes*	Yes*	Yes
		OR multiple reference sequences
PanCake [16]	Pan-genome data structure	Multiple reference sequences	External	Yes	Yes	No	No
		AND pairwise alignment
seq-seq-pan	Pan-genome data structure	Multiple reference sequences	External	Yes	Yes	Yes	Yes

^∗ Adding and removing of genomes in vg can be achieved using a combination of several steps