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
Category | Name | Input types (a, c, h, o, p, s, tx) | Description | Link | Paper |
|---|---|---|---|---|---|
De novo assembly | Cortex | s | Insertions, deletions, combinations of SNVs—inversions and deletions—rearrangements | [31] | |
SGVar | s | Large insertions and deletions, complex SV | Â | [32] | |
HySA | p, s | Small (11 to 50 bp) to large (> 50 bp) insertions and deletions, complex SV | [33] | ||
Assemblytics | a | Insertions and deletions (1 bp to 10 kb), repeat expansions/contractions | [34] | ||
Paftools | a | Insertions, deletions | [35] | ||
Smartie-sv | a | Insertions, deletions, inversions | [12] | ||
BreaKmer | s | Insertions, deletions, translocations, inversions, duplications | [36] | ||
novoBreak | s | Deletions, duplications, inversions, translocations | [37] | ||
Short-read mapping | BreakDancer | s | Deletions, insertions, inversions, intra-chromosomal and inter-chromosomal translocations | [38] | |
BreakSeq | Â | Insertions, deletions, translocations, inversions, duplications | [39] | ||
CREST | s | Insertions, deletions, translocations, inversions, duplications | [40] | ||
DELLY | s | Deletions, inversions, duplications, inter-chromosomal translocations | [41] | ||
EricScript | s | Gene fusion | [42] | ||
FusionCatcher | s | Gene fusion | [43] | ||
GRIDSS | s | Insertions, deletions, translocations, inversions, duplications | [44] | ||
Gustaf | s | Deletions, inversions, duplications, translocation | [45] | ||
IDP-fusion | p, s | Gene fusion | [46] | ||
JAFFA | p, s | Gene fusion | [47] | ||
LUMPY | s | Deletions, duplications, inversions, translocations | [48] | ||
Manta | s | Insertions, deletions, translocations, inversions, duplications | [49] | ||
Meerkat | s | Insertions, deletions, translocations, inversions, duplications | [50] | ||
Pindel | s | Insertions, deletions, translocations, inversions, duplications | [51] | ||
STAR-Fusion | s | Gene fusion | [52] | ||
SQUID | s | Gene fusion | [53] | ||
TARDIS | s | Discovery of tandem and interspersed segmental duplications | [54] | ||
TIGRA | s | Insertions, deletions | [55] | ||
Tophat-Fusion | s | Gene fusion | http://0-ccb-jhu-edu.brum.beds.ac.uk/software/tophat/fusion_index.shtml | [56] | |
Ulysses | s | Insertions, deletions, translocations, inversions, duplications | [57] | ||
SvABA | s | Insertion, deletions, somatic rearrangments | [58] | ||
Long-read mapping | NanoSV | o | Local SV (LSV): duplications, deletions, inversions; insertions (transposons, intra-chromosomal (> 1 Mb away) and inter-chromosomal insertions) | [59] | |
PBHoney | p | Insertions, deletions, duplications, inversions, translocations | [60] | ||
PBSV | p | Insertions (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-SV | p | Insertions, deletions, duplications, inversions, translocations | [61] | ||
Sniffles | o, p | Insertions, deletions, translocations, inversions, duplications, complex SV (nested SV) | [62] | ||
Multimethods SV caller | FusorSV | s | Combining LUMPY, DELLY, and GenomeSTRiP | [63] | |
MetaSV | s | Combining BreakSeq, Breakdancer, Pindel, CNVnator | [64] | ||
Parliament2 | s | Combining LUMPY, DELLY, Manta, BreakSeq, CNVnator | [65] | ||
SURVIVOR | a, o, p, s | Can combine/compare any SVs VCF | [10] | ||
Hi-C technology | Hic_breakfinder | h | Detects SVs based on optical mapping, Hi-C, short reads | [66] | |
HiCnv | h | Pipeline to identify CNVs from Hi-C data | [67] | ||
HiCtrans | h | Identify potential translocations using change-point statistics | [67] | ||
Optical mapping | Â | c | Commercial tools; visualization and analysis of Bionano data | https://bionanogenomics.com/support-page/bionano-access-software/ | Â |
Strand-Seq technology | Strandseq-InvertR | t | R package to locate putative inversions | [68] | |
10x Genomics | Gemtools | x | Downstream and in-depth analysis of SVs from linked-read data | [69] | |
GROC-SVs | x | Identify large-scale SVs based on barcode information | [70] | ||
LongRanger | x | Align reads, call and phase SNPs, indels, identify SVs | https://support.10xgenomics.com/genome-exome/software/downloads/latest | [16] | |
NAIBR | x | Identifies novel adjacencies created by SVs events | [71] |