BreakDancer protocols

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BreakDancer computational protocol

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

 (17)
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 breakdancer45, which cataloged deletions, insertions, inversions, and intra-chromosomal translocations., genetic distance was estimated using genome-wide snps46, where the distance between two […]

2017
PMCID: 5404267
PMID: 28440340
DOI: 10.1038/srep46759

[…] 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 […]

2017
PMCID: 5584659
PMID: 28890939
DOI: 10.1038/s41559-017-0242-3

[…] using gatk unifiedgenotyper40 and snpeff41, insertion sequences were identified using custom scripts and integrative genomics viewer42, and large genome-wide structural variants were detected using breakdancer43. mutations that were present in the ancestral clones were excluded, resulting in a set of mutations that were acquired during the selection experiment., populations that did not show […]

2017
PMCID: 5655702
PMID: 28247474
DOI: 10.1111/mec.14080

[…] 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 […]

2017
PMCID: 5693876
PMID: 29180989
DOI: 10.3389/fmicb.2017.02210

[…] 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; […]

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

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