Table 2.

SV detection algorithms.

Tool1	Platform	Method	Reference	Used in study
DELLY	IL	DP, SR	34	8,13,89,93
LUMPY	IL	DP, SR	35	8,81
Manta	IL	DP, SR, AS/l	36	89,94
GRIDSS	IL	DP, SR, AS/l	37,39
SvABA	IL, 10×	DP, SR, AS/l	38	13,83
Varlociraptor	IL	Post-processing	31
Lancet	IL		40
GROC-SVS	10×		95	81,83
Longranger	10×		96	81,83

Long read tools	Platform	Method	Reference	Cited by/remarks
HySA	PacBio and IL	Assembly and alignment	76	Hybrid assembly of IL and PacBio reads
SVIM	ONT, PacBio	Alignment	69	67,93,97
Sniffles	ONT, PacBio	Alignment	55	25,32,56,67,89,93,94,97,98
pbhoney	PacBio	Alignment	99	25,76
pbsv	PacBio	Alignment	100	25,97
NanoSV	ONT	Alignment	98	32,56,93
Picky	ONT	Alignment	56	32,93
NanoVar	ONT, PacBio	Alignment	93	Applied to a leukemia sample
cuteSV	ONT, PacBio	Alignment	97
nanomonsv	ONT	Alignment	68	Detects tumor-specific SVs

¹Inclusion criteria: published tool focussed on tumor-specific SV detection in cancer from tumor-normal paired WGS data, used in key studies addressed in this review. Long-read alignment based SV detection tools that are commonly used are included regardless of their ability to detect tumor-specific SVs.