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Table 1 Overview of multiple methods representative for the different SV methodologies currently used. Input types indicate the required data at start being either: De novo assembly (a), Oxford Nanopore (o), PacBio (p), 10X Genomics (x), Hi-C (h), Strand-Seq (t), Optical mapping (c) or Short reads (s)

From: Structural variant calling: the long and the short of it

CategoryNameInput types (a, c, h, o, p, s, tx)DescriptionLinkPaper
De novo assemblyCortexsInsertions, deletions, combinations of SNVs—inversions and deletions—rearrangements[31]
SGVarsLarge insertions and deletions, complex SV [32]
HySAp, sSmall (11 to 50 bp) to large (> 50 bp) insertions and deletions, complex SV[33]
AssemblyticsaInsertions and deletions (1 bp to 10 kb), repeat expansions/contractions[34]
PaftoolsaInsertions, deletions[35]
Smartie-svaInsertions, deletions, inversions[12]
BreaKmersInsertions, deletions, translocations, inversions, duplications[36]
novoBreaksDeletions, duplications, inversions, translocations[37]
Short-read mappingBreakDancersDeletions, insertions, inversions, intra-chromosomal and inter-chromosomal translocations[38]
BreakSeq Insertions, deletions, translocations, inversions, duplications[39]
CRESTsInsertions, deletions, translocations, inversions, duplications[40]
DELLYsDeletions, inversions, duplications, inter-chromosomal translocations[41]
EricScriptsGene fusion[42]
FusionCatchersGene fusion[43]
GRIDSSsInsertions, deletions, translocations, inversions, duplications[44]
GustafsDeletions, inversions, duplications, translocation[45]
IDP-fusionp, sGene fusion[46]
JAFFAp, sGene fusion[47]
LUMPYsDeletions, duplications, inversions, translocations[48]
MantasInsertions, deletions, translocations, inversions, duplications[49]
MeerkatsInsertions, deletions, translocations, inversions, duplications[50]
PindelsInsertions, deletions, translocations, inversions, duplications[51]
STAR-FusionsGene fusion[52]
SQUIDsGene fusion[53]
TARDISsDiscovery of tandem and interspersed segmental duplications[54]
TIGRAsInsertions, deletions[55]
Tophat-FusionsGene fusion[56]
UlyssessInsertions, deletions, translocations, inversions, duplications[57]
SvABAsInsertion, deletions, somatic rearrangments[58]
Long-read mappingNanoSVoLocal SV (LSV): duplications, deletions, inversions; insertions (transposons, intra-chromosomal (> 1 Mb away) and inter-chromosomal insertions)[59]
PBHoneypInsertions, deletions, duplications, inversions, translocations[60]
PBSVpInsertions (20 bp to 5 kb), deletions (20 bp to 100 kb), inversions (200 bp to 5 kb), intra-chromosomal (> 100 kb away) and inter-chromosomal translocations, complex SV 
SMRT-SVpInsertions, deletions, duplications, inversions, translocations[61]
Sniffleso, pInsertions, deletions, translocations, inversions, duplications, complex SV (nested SV)[62]
Multimethods SV callerFusorSVsCombining LUMPY, DELLY, and GenomeSTRiP[63]
MetaSVsCombining BreakSeq, Breakdancer, Pindel, CNVnator[64]
Parliament2sCombining LUMPY, DELLY, Manta, BreakSeq, CNVnator[65]
SURVIVORa, o, p, sCan combine/compare any SVs VCF[10]
Hi-C technologyHic_breakfinderhDetects SVs based on optical mapping, Hi-C, short reads[66]
HiCnvhPipeline to identify CNVs from Hi-C data[67]
HiCtranshIdentify potential translocations using change-point statistics[67]
Optical mapping cCommercial tools; visualization and analysis of Bionano data 
Strand-Seq technologyStrandseq-InvertRtR package to locate putative inversions[68]
10x GenomicsGemtoolsxDownstream and in-depth analysis of SVs from linked-read data[69]
GROC-SVsxIdentify large-scale SVs based on barcode information[70]
LongRangerxAlign reads, call and phase SNPs, indels, identify SVs[16]
NAIBRxIdentifies novel adjacencies created by SVs events[71]