ArticleBioinformatics (Oxford, England)2014
Probabilistic single-individual haplotyping.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Graph-based deep reinforcement learning for haplotype assembly with Ralphi.Genome research · 2025Article
- Methods for Chromosome-Scale Haplotype Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Direct inference of haplotypes from sequencing data.Bioinformatics advances · 2025Article
- Pairwise comparative analysis of six haplotype assembly methods based on users' experience.BMC genomic data · 2023Article
- XHap: haplotype assembly using long-distance read correlations learned by transformers.Bioinformatics advances · 2023Article
- HapCUT2: A Method for Phasing Genomes Using Experimental Sequence Data.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Experimental method for haplotype phasing across the entire length of chromosome 21 in trisomy 21 cells using a chromosome elimination technique.Journal of human genetics · 2022Article
- Computational methods for chromosome-scale haplotype reconstruction.Genome biology · 2021Review
- A Long-Read Sequencing Approach for Direct Haplotype Phasing in Clinical Settings.International journal of molecular sciences · 2020Article
- ComHapDet: a spatial community detection algorithm for haplotype assembly.BMC genomics · 2020Article
- A chaotic viewpoint-based approach to solve haplotype assembly using hypergraph model.PloS one · 2020Article
- Minimum error correction-based haplotype assembly: Considerations for long read data.PloS one · 2020Article
- Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing.Nature communications · 2019Article
- Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes.Bioinformatics (Oxford, England) · 2019Article
- Haplotype-aware diplotyping from noisy long reads.Genome biology · 2019Article
- GenHap: a novel computational method based on genetic algorithms for haplotype assembly.BMC bioinformatics · 2019Article
- NGS based haplotype assembly using matrix completion.PloS one · 2019Article
- HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads.BMC bioinformatics · 2018Article
- Article
- An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments.Bioinformatics (Oxford, England) · 2018Article
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Authors and funding
1 author.
Funding
Abstract
motivationAccurate haplotyping-determining from which parent particular portions of the genome are inherited-is still mostly an unresolved problem in genomics. This problem has only recently started to become tractable, thanks to the development of new long read sequencing technologies. Here, we introduce ProbHap, a haplotyping algorithm targeted at such technologies. The main algorithmic idea of ProbHap is a new dynamic programming algorithm that exactly optimizes a likelihood function specified by a probabilistic graphical model and which generalizes a popular objective called the minimum error correction. In addition to being accurate, ProbHap also provides confidence scores at phased positions.
resultsOn a standard benchmark dataset, ProbHap makes 11% fewer errors than current state-of-the-art methods. This accuracy can be further increased by excluding low-confidence positions, at the cost of a small drop in haplotype completeness. AVAILABILITY: Our source code is freely available at: https://github.com/kuleshov/ProbHap.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.