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A breakpoint-based algorithm, which can unbiasedly and efficiently detect both homozygous and heterozygous INDELs, ranging from several base pairs to over thousands of base pairs, with accurate breakpoint and heterozygosity rate estimations. Comprehensive evaluations on both simulated and real datasets revealed that BreakSeek outperformed other existing methods on both sensitivity and specificity in detecting both small and large INDELs, and uncovered a significant amount of novel INDELs that were missed before.

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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Maintainer

  • Fangqing Zhao <zhfq at mail.biols.ac.cn>

Institution(s)

Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China

Funding source(s)

NSFC [91131013, 31100952]; CAS grants

  • (Zhao and Fangqing, 2015) BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection. Nucleic Acids Research.
    DOI: 10.1093/nar/gkv605
  • (Neuman et al., 2013) Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in bioinformatics.
    PMID: 22707752

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