ArticleBMC genomics2018
Efficient algorithms for polyploid haplotype phasing.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.International journal of molecular sciences · 2025Article
- GCphase: an SNP phasing method using a graph partition and error correction algorithm.BMC bioinformatics · 2024Article
- Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.Frontiers in genetics · 2023Article
- PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.BMC bioinformatics · 2022Article
- Multiallelic models for QTL mapping in diverse polyploid populations.BMC bioinformatics · 2022Article
- nPhase: an accurate and contiguous phasing method for polyploids.Genome biology · 2021Article
- Haplotype threading: accurate polyploid phasing from long reads.Genome biology · 2020Article
- Hap10: reconstructing accurate and long polyploid haplotypes using linked reads.BMC bioinformatics · 2020Article
- The effect of autopolyploidy on population genetic signals of hard sweeps.Biology letters · 2020Article
- Breeding Top Genotypes and Accelerating Response to Recurrent Selection by Selecting Parents with Greater Gametic Variance.Genetics · 2020Article
- Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization.BMC genomics · 2019Article
- Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis.Genome biology · 2019Article
- Lager-brewing yeasts in the era of modern genetics.FEMS yeast research · 2019Review
- pSBVB: A Versatile Simulation Tool To Evaluate Genomic Selection in Polyploid Species.G3 (Bethesda, Md.) · 2019Article
- A graph-based algorithm for estimating clonal haplotypes of tumor sample from sequencing data.BMC medical genomics · 2019Article
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4 authors.
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Abstract
backgroundInference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component for many analyses including admixture mapping, identifying regions of identity by descent and imputation. Haplotype phasing based on sequencing reads has attracted lots of attentions. Diploid haplotype phasing where the two haplotypes are complimentary have been studied extensively. In this work, we focused on Polyploid haplotype phasing where we aim to phase more than two haplotypes at the same time from sequencing data. The problem is much more complicated as the search space becomes much larger and the haplotypes do not need to be complimentary any more.
resultsWe proposed two algorithms, (1) Poly-Harsh, a Gibbs Sampling based algorithm which alternatively samples haplotypes and the read assignments to minimize the mismatches between the reads and the phased haplotypes, (2) An efficient algorithm to concatenate haplotype blocks into contiguous haplotypes.
conclusionsOur experiments showed that our method is able to improve the quality of the phased haplotypes over the state-of-the-art methods. To our knowledge, our algorithm for haplotype blocks concatenation is the first algorithm that leverages the shared information across multiple individuals to construct contiguous haplotypes. Our experiments showed that it is both efficient and effective.
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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.