Table 1.

Comparison of KOMB to previous tools developed for CNV detection in Metagenomes. KOMB utilizes a fully connected hybrid unitig graph based on repeat linkage to track CNV across samples. Only the central algorithms for repeat detection and/or SV detection are listed as some tools use a combination of algorithms. Abbreviations: BinEM = Bernoulli Mixture Model (BMM) estimated through the Expectation–Maximization (EM), NEM  = Neighboring Expectation–Maximization algorithm, Bet. Centrality  = Betweenness Centrality

Tool	Algorithm	Linear	Reference	Detect	Works	Anomaly
		Time	free	CNV	on	Detection
		Complexity			Raw Reads
PPanGGOLiN [55]	BinEM/NEM	No	No	Yes	No	No
Bambus2 [29]	Bet. Centrality	No	Yes	Yes	Yes	No
MetaCarvel [31]	Approx. Bet.Centrality	Approx.	Yes	Yes	Yes	No
KOMB (this work)	K-core Decomposition	Yes	Yes	Yes	Yes	Yes