ArticlePloS one2019
NGS based haplotype assembly using matrix completion.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- EvANI benchmarking workflow for evolutionary distance estimation.Briefings in bioinformatics · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.bioRxiv : the preprint server for biology · 2025Article
- Pairwise comparative analysis of six haplotype assembly methods based on users' experience.BMC genomic data · 2023Article
- Hap10: reconstructing accurate and long polyploid haplotypes using linked reads.BMC bioinformatics · 2020Article
- Minimum error correction-based haplotype assembly: Considerations for long read data.PloS one · 2020Article
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Authors and funding
2 authors.
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Abstract
We apply matrix completion methods for haplotype assembly from NGS reads to develop the new HapSVT, HapNuc, and HapOPT algorithms. This is performed by applying a mathematical model to convert the reads to an incomplete matrix and estimating unknown components. This process is followed by quantizing and decoding the completed matrix in order to estimate haplotypes. These algorithms are compared to the state-of-the-art algorithms using simulated data as well as the real fosmid data. It is shown that the SNP missing rate and the haplotype block length of the proposed HapOPT are better than those of HapCUT2 with comparable accuracy in terms of reconstruction rate and switch error rate. A program implementing the proposed algorithms in MATLAB is freely available at https://github.com/smajidian/HapMC.
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Registered trials
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