Table 3 The user recommendation table

From: Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data

DEL and INS (p = 0 P = 0.5 r = 500 O = 0) (Pacbio)	size range	SV type	top1	top2	top3	top4	top5
	50 bp–1 kb	DEL	cuteSV	Sniffles2	MAMnet	Sniffles	SVIM
	50 bp–1 kb	INS	SKSV	INSnet	MAMnet	PAV	cuteSV
	1 kb–10 kb	DEL	cuteSV	PAV	DeBreak	SKSV	Smartie-sv_asm
	1 kb–10 kb	INS	PAV	SKSV	Smartie-sv_asm	SVIM-asm	pbsv
	≥10 kb	DEL	SKSV	cuteSV	SVIM	SVIM-asm	PAV
	≥10 kb	INS	Dipcall	PAV	DeBreak	SVIM-asm	Smartie-sv_asm
	≥50 bp	DEL	cuteSV	DeBreak	Sniffles	SKSV	MAMnet
	≥50 bp	INS	SKSV	INSnet	PAV	MAMnet	cuteSV
	coverage	SV type	top1	top2	top3	top4	top5
	5×	DEL	MAMnet	pbsv	PBHoney	Sniffles2	Smartie-sv_aln
	5×	INS	MAMnet	Sniffles2	pbsv	Smartie-sv_aln	NanoSV
	10×	DEL	MAMnet	pbsv	PBHoney	Sniffles2	Smartie-sv_aln
	10×	INS	MAMnet	Sniffles2	Smartie-sv_aln	Smartie-sv_asm	PAV
	20×	DEL	DeBreak	Sniffles2	MAMnet	PAV	pbsv
	20×	INS	DeBreak	MAMnet	PAV	Sniffles2	SVIM-asm
	≥30×	DEL	DeBreak	MAMnet	Sniffles2	PAV	cuteSV
	≥30×	INS	DeBreak	MAMnet	Sniffles2	INSnet	PAV
Complex SV (TRA, INV and DUP) (Pacbio)	data type	SV type	top1	top2	top3	top4	top5
	Simulation data (Hifi/CLR)	TRA	NanoSV/cuteSV	cuteSV/pbsv	pbsv/NanoSV	SVIM/SVIM	SKSV/NanoVar
		INV	NanoVar/Sniffles2	SVIM/cuteSV	cuteSV/SVIM	Sniffles/NanoVar	Sniffles2/Sniffles
		DUP	pbsv/pbsv	DeBreak/NanoVar	NanoVar/Sniffles2	Sniffles2/DeBreak	SVision/NanoSV
	data type	SV type	top1	top2	top3	top4	top5
	Real cancer data (CLR)	TRA	pbsv	cuteSV	Sniffles	Sniffles2	SVIM
		INV	pbsv	SVIM	Sniffles2	SVIM-asm	DeBreak
		DUP	DeBreak	Sniffles2	Sniffles	cuteSV	pbsv
DEL and INS (p = 0 P = 0.5 r = 500 O = 0) (ONT)	size range	SV type	top1	top2	top3	top4	top5
	5 bp–1 kb	DEL	PAV	cuteSV	SVIM	SVIM-asm	SVision
	5 bp–1 kb	INS	MAMnet	DeBreak	cuteSV	Sniffles2	PAV
	1 kb–10 kb	DEL	DeBreak	PAV	Sniffles	Sniffles2	cuteSV
	1 kb–10 kb	INS	DeBreak	cuteSV	PAV	MAMnet	Sniffles2
	≥10 kb	DEL	SVision	Sniffles	cuteSV	DeBreak	Sniffles2
	≥10 kb	INS	DeBreak	cuteSV	PAV	MAMnet	SVision
	≥50 bp	DEL	PAV	cuteSV	SVIM	SVIM-asm	SVision
	≥50 bp	INS	cuteSV	MAMnet	DeBreak	Sniffles2	PAV
	coverage	SV type	top1	top2	top3	top4	top5
	5×	DEL	Sniffles2	NanoVar	PAV	Smartie-sv_aln	DeBreak
	5×	INS	Sniffles2	PAV	NanoVar	NanoSV	DeBreak
	10×	DEL	Sniffles2	DeBreak	NanoVar	SVIM-asm	SVision
	10×	INS	Sniffles2	DeBreak	SVIM-asm	SVision	NanoSV
	20×	DEL	PAV	Sniffles2	SVision	MAMnet	SVIM-asm
	20×	INS	MAMnet	DeBreak	Sniffles2	PAV	SVIM-asm
	≥30×	DEL	PAV	SVIM-asm	Sniffles2	cuteSV	SVIM
	≥30×	INS	MAMnet	DeBreak	Sniffles2	PAV	cuteSV
Complex SV (TRA, INV, and DUP) (ONT)	data type	SV type	top1	top2	top3	top4	top5
	Simulation data (ONT)	TRA	cuteSV	NanoSV	SVIM	NanoVar	SVIM-asm
		INV	NanoVar	SVIM	cuteSV	Sniffles2	Sniffles
		DUP	NanoVar	SVision	Sniffles2	DeBreak	cuteSV
	data type	SV type	top1	top2	top3	top4	top5
	Real cancer data (ONT)	TRA	NanoSV	Sniffles2	NanoVar	SVIM-asm	cuteSV
		INV	NanoSV	Sniffles2	Debreak	SVIM-asm	NanoVar
		DUP	Debreak	NanoVar	Sniffles2	SVision	NanoSV
Overall performance across datasets for DEL and INS (p = 0 P = 0.5 r = 500 O = 0)	Data type	SV type	top1	top2	top3	top4	top5
	Hifi	DEL	DeBreak	Sniffles2	PAV	SVIM-asm	pbsv
	Hifi	INS	DeBreak	PAV	INSnet	MAMnet	SVIM-asm
	CLR	DEL	cuteSV	DeBreak	Sniffles2	pbsv	Sniffles
	CLR	INS	DeBreak	MAMnet	cuteSV	SVIM-asm	INSnet
	Nano	DEL	cuteSV	SVIM	Sniffles2	MAMnet	SVIM-asm
	Nano	INS	cuteSV	MAMnet	DeBreak	Sniffles2	INSnet
	Data type	SV type	top1	top2	top3	top4	top5
	Hifi gt	DEL	PAV	Sniffles2	SVIM-asm	pbsv	cuteSV
	Hifi gt	INS	PAV	SVIM-asm	cuteSV	Sniffles2	DeBreak
	CLR gt	DEL	cuteSV	Sniffles2	pbsv	DeBreak	SVIM
	CLR gt	INS	cuteSV	DeBreak	SVIM-asm	PAV	Sniffles2
	Nano gt	DEL	cuteSV	Sniffles2	SVIM	SVIM-asm	DeBreak
	Nano gt	INS	cuteSV	Sniffles2	DeBreak	SVIM-asm	PAV

For each evaluation scenario, the table lists several fine-grained conditions and the top 1–5 methods.

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Table 3 The user recommendation table

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