Comparison of multiple algorithms to reliably detect structural variants in pears

BMC Genomics

Table 1 Comparison of the nine types of SV detection software

Data type	Detection tools	Detectable SV types								Algorithms
Data type	Detection tools	INS	DEL	INV	DUP	ITX	CTX	TRA	MNPs	Algorithms
Illumina data	Pindel	Yes	Yes	Yes	Yes	No	No	No	No	SR
	BreakDancer	Yes	Yes	Yes	No	Yes	Yes	No	No	RP
	DELLY	Yes	Yes	Yes	Yes	No	No	Yes	No	RP + SR
	IMR/DENOM	Yes	Yes	No	No	No	No	No	No	AS
	LUMPY	No	Yes	Yes	Yes	No	No	Yes	No	RP + SR
	Platypus	Yes	Yes	No	No	No	No	No	Yes	AS
	MetaSV	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	–
PacBio data	Sniffles	Yes	Yes	Yes	Yes	No	No	Yes	No	SR
PacBio data	SVIM	Yes	Yes	Yes	Yes	No	No	No	No	SR

Notes. An overview of the nine SV callers, including the types of SVs detected (INS: insertion, DEL: deletion, INV: inversion, DUP: duplication, TRA: Translocation, ITX: intra-chromosomal translocation, CTX: inter-chromosomal translocation) and the mutation signals used (SR: split reads, RP: read pairs, AS: assembly). The symbol ‘-’ indicates that the algorithm is chosen by the user

ISSN: 1471-2164