SVDetect statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SVDetect

Tool usage distribution map

This map represents all the scientific publications referring to SVDetect per scientific context
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Associated diseases

This word cloud represents SVDetect usage per disease context

Popular tool citations

chevron_left Structural variant detection CNV detection Deletion detection Insertion detection Duplication detection Inversion detection chevron_right
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SVDetect specifications


Unique identifier OMICS_00324
Name SVDetect
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.8b
Stability Stable
Maintained Yes




No version available


  • person_outline SVDetect Team

Publication for SVDetect

SVDetect citations


The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease

PMCID: 5823580
PMID: 29492199
DOI: 10.18632/oncotarget.23614
call_split See protocol

[…] a total of 167 million reads which, after mapping with stampy [] (version 1.0.13), resulted in a genome wide coverage of 8.65 fold with a local coverage of the transgene of 18.34 fold . Subsequently SVDetect [] (version 0.7) was used in interchromosomal rearrangement mode to identify the integration site of the ALK transgene vector. […]


Breakpoint mapping and haplotype analysis of translocation t(1;12)(q43;q21.1) in two apparently independent families with vascular phenotypes

PMCID: 5823676
PMID: 29168350
DOI: 10.1002/mgg3.346

[…] Aligner (BWA) (Li & Durbin, ). To annotate the unique SVs, reads not aligning uniquely, were removed and the ones with unexpected orientation or aligning to different chromosomes were extracted using SVDetect ( et al., ) and Delly ( The predicted SVs were compared with multiple in‐house mate pair datasets to identify sampl […]


Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate Pair Sequencing

PLoS One
PMCID: 5225008
PMID: 28072833
DOI: 10.1371/journal.pone.0169935

[…] nd reads to the human reference genome GRCh37/hg19 using Burrows-Wheeler Aligner (BWA)-MEM with default parameters []. Reads not aligning uniquely as well as PCR duplicates were not analysed further. SVDetect was then used to identify potential translocations, inversions and large deletions/insertions from discordant paired-end data [] aligning on different chromosomes, with unexpected strand orie […]


A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease

Hum Genomics
PMCID: 5116179
PMID: 27863505
DOI: 10.1186/s40246-016-0092-0

[…] For detecting structural variations, mate-pair reads obtained by SOLiD 5500xl System were analyzed by svdetect (version r0.8b) []. […]


Genome wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

BMC Plant Biol
PMCID: 4845489
PMID: 27118394
DOI: 10.1186/s12870-016-0788-2
call_split See protocol

[…] ce genomes allowing two mismatches. The software bwa v0.5.7-r1310 was used to align the cleaned DXWR DNA reads to the Nipponbare genome for SV detection. SV detection was conducted using the software SVDetect v0.8b []. The pipeline SVFilter was developed in Fei’s lab, Cornell University, which can be downloaded from This paper is required to be cited […]


Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products

Anal Bioanal Chem
PMCID: 4909802
PMID: 27100228
DOI: 10.1007/s00216-016-9549-1

[…] s. First the reads were aligned to the reference mouse genome with use of Bowtie [, ] in global (end-to-end reads alignment) and local (soft clipped reads) modes, with the software programs DELLY and SVDetect [, ]. Unique and discordantly mapped reads were further analyzed to detect structural variants after filtering to remove repeats, mitochondria, centromeres, and intrachromosomal rearrangement […]

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SVDetect institution(s)
Institut Curie, Paris, France; INSERM, U900, Paris, France; Mines ParisTech, Fontainebleau, France; INSERM, U380, Paris, France; CNRS, UMR3244, Université Pierre et Marie Curie, Paris, France
SVDetect funding source(s)
Supported by ‘Projet Incitatif Collaboratif Bioinformatique et Biostatistiques’ of the Institut Curie; Ligue Nationale Contre le Cancer; Institut National du Cancer.

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