Table 1 Summary of BFB detection tools

Tool	LGM-resolved	Feature					Experiment data protocol
		CN	BP	FBI	DEL/DUP INS/TRX	Virus	aCGH	PE	10x	PB	ONT	OM	SC
Kinsella et al.²²	✓	✓	–	–	–	–	✓	–	–	–	–	–	–
BFBFinder^23,24	✓	✓	–	+	–	–	✓	✓	–	–	–	–	–
Greenman et al.^25,26	✓	✓	✓	–	–	–	–	✓	–	–	–	–	–
AA + AC¹⁹	–	✓	✓	✓	✓	+	–	✓	–	–	–	–	–
AR²⁰	✓	✓	✓	✓	✓	+	–	–	–	–	–	✓	–
LINX²¹	✓	✓	✓	✓	✓	+	–	✓	–	–	–	–	–
Ambigram	✓	✓	✓	✓	✓	✓	–	✓	✓	✓	✓	✓	✓

"✓” for available and “–” for not applicable. The FBI feature of Zakov et al. is marked by “+” since Zakov et al. solves the BFB using the CN count vector first, then uses the FBI fraction to verify the confidence of the BFB. Greenman et al. solely use FBI breakpoints, neglecting the head-to-head or tail-to-tail direction of the FBI. The virus feature of the complex rearrangement detection pipelines AA + AC, AR, and LINX are indicated by “+” because they resolve BFB and virus integration individually rather than correlating BFB and viral integration into one evolution process. BFB breakage-fusion-bridge, LGM local genomic map, CN copy number, BP breakpoint, FBI fold-back inversion, DEL deletion, DUP duplication, INS insertion, TRX translocation, aCGH array comparative genomic hybridization, PE paired-end, 10x 10x linked-reads, PB PacBio, ONT Oxford Nanopore, OM optical mapping, SC single cell, AA AmpliconArchitect, AC AmpliconClassifier, AR AmpliconReconstructor.

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