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An approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants.

Specifications

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Programming languages:
Python
Computer skills:
Advanced
Stability:
Stable
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Publications

  • (Abo et al., 2014) BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers. Nucleic acids research.
    PMID: 25428359

Classification

Literature

  • (Treangen and Salzberg, 2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature reviews Genetics.
    PMID: 22124482
  • (Cao et al., 2014) Sequencing technologies and tools for short tandem repeat variation detection. Briefings in bioinformatics.
    PMID: 24504770

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