SVDetect statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SVDetect
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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
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Popular tool citations

chevron_left Structural variant detection CNV detection Deletion detection Insertion detection Duplication detection Inversion detection chevron_right
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Protocols

SVDetect specifications

Information


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

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  • person_outline SVDetect Team

Publication for SVDetect

SVDetect citations

 (22)
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The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease

2017
Oncotarget
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. […]

library_books

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

2017
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 (http://svdetect.sourceforge.net/)(Zeitouni et al., ) and Delly (www.korbel.embl.de/software.html). The predicted SVs were compared with multiple in‐house mate pair datasets to identify sampl […]

library_books

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

2017
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 […]

library_books

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

2016
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) []. […]

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

2016
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 http://bioinfo.bti.cornell.edu/tool/SVFilter/. This paper is required to be cited […]

library_books

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

2016
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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