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Popular tool citations

chevron_left Structural variant detection Deletion detection Insertion detection Inter-chromosomal translocation detection Inversion detection Intra-chromosomal translocation detection chevron_right
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BreakDancer specifications

Information


Unique identifier OMICS_00307
Name BreakDancer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Alignment files
Operating system Unix/Linux
Programming languages C++, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Ken Chen <>

Publication for BreakDancer

BreakDancer in pipelines

 (31)
2018
PMCID: 5780457
PMID: 29362368
DOI: 10.1038/s41598-018-19278-1

[…] if the afs for all the other 23 samples were <5%. the candidate mutation site was defined as homozygous if the af ≥80%, and if the afs for all the other 23 samples were <5%. for the pindel and breakdancer analyses, the candidate mutation sites were sorted by the position in the genome and those unique to a single sample were further considered. all candidate mutations were confirmed […]

2018
PMCID: 5844311
PMID: 29326229
DOI: 10.1534/g3.117.300421

[…] effect of the variation ()., to detect genomic svs from high-throughput sequencing data, the r. mackenziei strains ihm 22877 and dh24460 were analyzed combining two different methods. first, we ran breakdancer () to predict sv based on paired-end read mapping (default parameters). to increase the sensitivity and specificity of the call, we used the output of breakdancer as input for pindel (), […]

2018
PMCID: 5880257
PMID: 29610388
DOI: 10.1101/mcs.a002279

[…] frequency (baf) outputs, were analyzed and events flagged and visualized using nexus discovery edition 7.5 (biodiscovery, inc., el segundo, ca)., translocation events were investigated using breakdancer (v1.4.5). analysis was limited to a set of cancer-specific genes, as previously defined ()., presence of hpv was determined by alignment of tumor sample reads using bwa (). hpv […]

2018
PMCID: 5917405
PMID: 29725344
DOI: 10.3389/fpls.2018.00508

[…] (). the snpeff binary database file (.bin) was generated using the b. napus darmor-bzh genome annotation file v5 (gff3) and the whole genome reference sequence ()., after initial quality control by breakdancer (), 15 samples were excluded from further analysis as the coefficient of variation of the insert size exceeded the cutoff value of 1. as such, 134 samples had sufficiently high quality […]

2018
PMCID: 5923208
PMID: 29703940
DOI: 10.1038/s41467-018-04093-z

[…] we further filtered snps with more than 10% samples with missing genotypes, or deviated from hardy-weinberg principle in some downstream analysis. structural variants (sv) were identified using breakdancer, which cataloged deletions, insertions, inversions, and intra-chromosomal translocations., genetic distance was estimated using genome-wide snps, where the distance between two […]


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BreakDancer in publications

 (174)
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004

[…] against the human reference sequence grch37/hg19. quality control (qc), variant annotation, deduplication and metrics were generated for each sample. manta (https://github.com/illumina/manta) and breakdancer (breakdancer.sourceforge.net) were used for the detection of structural variants., methylation data from the illumina infinium humanmethylation450 beadchip was preprocessed using […]

PMCID: 5941560
PMID: 29739316
DOI: 10.1186/s12864-018-4718-6

[…] a certain type of sequence information to identify specific categories of variants. our variant caller suite consisted of four distinct tools and algorithms: the genome analysis toolkit, pindel, breakdancer, and cnvnator [–]., the genome analysis toolkit (gatk) from the broad institute uses de bruijn graph-based models to identify single-nucleotide substitutions and small insertions […]

PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] the rice sv data obtained by calling against the nipponbare reference genome using novobreak because it had the lowest false positive rate when compared with results from several tools such as breakdancer and delly. this sv data set contains a total number of 93,683 svs (deletions, inversions and duplications of >100 bps and <1 mbps, and translocations), or an average of 12,178 svs […]

PMCID: 5917405
PMID: 29725344
DOI: 10.3389/fpls.2018.00508

[…] more common than transversions with 57% and 43% respectively. of the 101,040 genes described in the darmor-bzh reference, 76,419 contained at least one snp., the average number of svs identified by breakdancer and pindel, as well as the number of unique svs remaining after each filtering step is provided in supplementary table . analysis of svs in canola revealed that deletions were more common […]

PMCID: 5880257
PMID: 29610388
DOI: 10.1101/mcs.a002279

[…] frequency (baf) outputs, were analyzed and events flagged and visualized using nexus discovery edition 7.5 (biodiscovery, inc., el segundo, ca)., translocation events were investigated using breakdancer (v1.4.5). analysis was limited to a set of cancer-specific genes, as previously defined ()., presence of hpv was determined by alignment of tumor sample reads using bwa (). hpv […]


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BreakDancer institution(s)
The Genome Center, Washington University School of Medicine, St Louis, MO, USA

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