BreakDancer pipeline

BreakDancer specifications


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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  • person_outline Ken Chen <>

Publication for BreakDancer

BreakDancer citations

PMCID: 5923208

[…] 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 breakdancer45, which cataloged deletions, insertions, inversions, and intra-chromosomal translocations., genetic distance was estimated using genome-wide snps46, where the distance between two […]

PMCID: 5693876

[…] ca, united states). the average sequencing depth was around 110x. to detect genetic alterations, clean reads obtained from genome sequencing were mapped to the reference genome of gt1, and samtools, breakdancer and cnvnator were used to detect short indels, structural variations (insertion, deletion, and inversion) and copy number variations, respectively (chen et al., 2009; li et al., 2009; […]

PMCID: 5701311

[…] (the international hapmap consortium 2003), and 1000 genomes projects (the 1000 genomes project consortium 2015). bioinformatic identification of cnvs was performed using default parameters of breakdancer (v 1.4.5) (chen et al. 2009) and cnvnator (v 0.3) (abyzov et al. 2011)., wgs alignments and regional variation in read coverage were viewed using the integrated genomics viewer (igv, […]

PMCID: 5404267

[…] translocation of the large segments in the genome level. the insertion, deletion, inversion, intra-chromosomal translocation and inter translocation between the reference and the sample are found by breakdancer software49., cells cultured in different carbon source of logarithmic growth phase were quenched and extracted as intracellular metabolites according to our previous method14. an extra […]

PMCID: 5655702

[…] the illumina miseq platform and reads aligned using bwa. small variants (snps and small indels) were identified using gatk haplotypecaller and snpeff and structural rearrangements identified using breakdancer. a list of all mutational targets is given in table s2 (supporting information)., to investigate the dynamics of compensatory mutations associated with plasmid amelioration, we screened […]

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

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