ArticleNucleic acids research2015
BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Comparative Genomics Insights Into the Evolutionary Disparities Between Nitroplast-Evolved Ecotype UCYN-A2 and Its Closest Relative UCYN-A1.Ecology and evolution · 2025Article
- INSnet: a method for detecting insertions based on deep learning network.BMC bioinformatics · 2023Article
- SIns: A Novel Insertion Detection Approach Based on Soft-Clipped Reads.Frontiers in genetics · 2021Article
- Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing.Genome biology · 2019Article
- GPA: A Microbial Genetic Polymorphisms Assignments Tool in Metagenomic Analysis by Bayesian Estimation.Genomics, proteomics & bioinformatics · 2019Article
- Combining probabilistic alignments with read pair information improves accuracy of split-alignments.Bioinformatics (Oxford, England) · 2018Article
- Precision Medicine: What Challenges Are We Facing?Genomics, proteomics & bioinformatics · 2016Article
- SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.BMC systems biology · 2016Article
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2 authors.
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Abstract
Although recent developed algorithms have integrated multiple signals to improve sensitivity for insertion and deletion (INDEL) detection, they are far from being perfect and still have great limitations in detecting a full size range of INDELs. Here we present BreakSeek, a novel 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. In addition, by incorporating sophisticated statistic models, we for the first time investigated and demonstrated the importance of handling false and conflicting signals for multi-signal integrated methods.
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