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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—rearrangementshttp://cortexassembler.sourceforge.net/[31]
SGVarsLarge insertions and deletions, complex SV [32]
HySAp, sSmall (11 to 50 bp) to large (> 50 bp) insertions and deletions, complex SVhttps://bitbucket.org/xianfan/hybridassemblysv/overview[33]
AssemblyticsaInsertions and deletions (1 bp to 10 kb), repeat expansions/contractionshttps://github.com/MariaNattestad/Assemblytics[34]
PaftoolsaInsertions, deletionshttps://github.com/lh3/minimap2/tree/master/misc[35]
Smartie-svaInsertions, deletions, inversionshttps://github.com/zeeev/smartie-sv[12]
BreaKmersInsertions, deletions, translocations, inversions, duplicationshttps://github.com/ccgd-profile/BreaKmer[36]
novoBreaksDeletions, duplications, inversions, translocationshttps://sourceforge.net/projects/novobreak/[37]
Short-read mappingBreakDancersDeletions, insertions, inversions, intra-chromosomal and inter-chromosomal translocationshttps://github.com/genome/breakdancer[38]
BreakSeq Insertions, deletions, translocations, inversions, duplicationshttp://sv.gersteinlab.org/breakseq/[39]
CRESTsInsertions, deletions, translocations, inversions, duplicationshttps://www.stjuderesearch.org/site/lab/zhang[40]
DELLYsDeletions, inversions, duplications, inter-chromosomal translocationshttps://github.com/dellytools/delly[41]
EricScriptsGene fusionhttps://sourceforge.net/projects/ericscript/[42]
FusionCatchersGene fusionhttps://github.com/ndaniel/fusioncatcher[43]
GRIDSSsInsertions, deletions, translocations, inversions, duplicationshttps://github.com/PapenfussLab/gridss[44]
GustafsDeletions, inversions, duplications, translocationhttp://www.seqan.de/apps/gustaf/[45]
IDP-fusionp, sGene fusionhttps://www.healthcare.uiowa.edu/labs/au/IDP-fusion/[46]
JAFFAp, sGene fusionhttps://github.com/Oshlack/JAFFA/wiki[47]
LUMPYsDeletions, duplications, inversions, translocationshttps://github.com/arq5x/lumpy-sv[48]
MantasInsertions, deletions, translocations, inversions, duplicationshttps://github.com/Illumina/manta[49]
MeerkatsInsertions, deletions, translocations, inversions, duplicationshttp://compbio.med.harvard.edu/Meerkat/[50]
PindelsInsertions, deletions, translocations, inversions, duplicationshttps://github.com/genome/pindel[51]
STAR-FusionsGene fusionhttps://github.com/STAR-Fusion/STAR-Fusion/wiki[52]
SQUIDsGene fusionhttps://github.com/Kingsford-Group/squid[53]
TARDISsDiscovery of tandem and interspersed segmental duplicationshttps://github.com/BilkentCompGen/tardis[54]
TIGRAsInsertions, deletionshttps://bitbucket.org/xianfan/tigra[55]
Tophat-FusionsGene fusionhttp://ccb.jhu.edu/software/tophat/fusion_index.shtml[56]
UlyssessInsertions, deletions, translocations, inversions, duplicationshttps://github.com/gillet/ulysses[57]
SvABAsInsertion, deletions, somatic rearrangmentshttps://github.com/walaj/svaba[58]
Long-read mappingNanoSVoLocal SV (LSV): duplications, deletions, inversions; insertions (transposons, intra-chromosomal (> 1 Mb away) and inter-chromosomal insertions)https://github.com/mroosmalen/nanosv[59]
PBHoneypInsertions, deletions, duplications, inversions, translocationshttps://sourceforge.net/projects/pb-jelly/[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 SVhttps://github.com/PacificBiosciences/pbsv 
SMRT-SVpInsertions, deletions, duplications, inversions, translocationshttps://github.com/EichlerLab/pacbio_variant_caller[61]
Sniffleso, pInsertions, deletions, translocations, inversions, duplications, complex SV (nested SV)https://github.com/fritzsedlazeck/Sniffles[62]
Multimethods SV callerFusorSVsCombining LUMPY, DELLY, and GenomeSTRiPhttps://github.com/TheJacksonLaboratory/SVE[63]
MetaSVsCombining BreakSeq, Breakdancer, Pindel, CNVnatorhttp://bioinform.github.io/metasv/[64]
Parliament2sCombining LUMPY, DELLY, Manta, BreakSeq, CNVnatorhttps://github.com/dnanexus/parliament2[65]
SURVIVORa, o, p, sCan combine/compare any SVs VCFhttps://github.com/fritzsedlazeck/SURVIVOR[10]
Hi-C technologyHic_breakfinderhDetects SVs based on optical mapping, Hi-C, short readshttps://github.com/dixonlab/hic_breakfinder[66]
HiCnvhPipeline to identify CNVs from Hi-C datahttps://github.com/ay-lab/HiCnv[67]
HiCtranshIdentify potential translocations using change-point statisticshttps://github.com/ay-lab/HiCtrans[67]
Optical mapping cCommercial tools; visualization and analysis of Bionano datahttps://bionanogenomics.com/support-page/bionano-access-software/ 
Strand-Seq technologyStrandseq-InvertRtR package to locate putative inversionshttps://sourceforge.net/projects/strandseq-invertr/[68]
10x GenomicsGemtoolsxDownstream and in-depth analysis of SVs from linked-read datahttps://github.com/sgreer77/gemtools[69]
GROC-SVsxIdentify large-scale SVs based on barcode informationhttps://github.com/grocsvs/grocsvs[70]
LongRangerxAlign reads, call and phase SNPs, indels, identify SVshttps://support.10xgenomics.com/genome-exome/software/downloads/latest[16]
NAIBRxIdentifies novel adjacencies created by SVs eventshttps://github.com/raphael-group/NAIBR[71]