ArticleBMC genomics2015
SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- nTChap: an accurate method for polyploid haplotype reconstruction.BMC genomics · 2026Article
- Methods for Chromosome-Scale Haplotype Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- GCphase: an SNP phasing method using a graph partition and error correction algorithm.BMC bioinformatics · 2024Article
- Pairwise comparative analysis of six haplotype assembly methods based on users' experience.BMC genomic data · 2023Article
- Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences.Systematic biology · 2023Article
- XHap: haplotype assembly using long-distance read correlations learned by transformers.Bioinformatics advances · 2023Article
- Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.Frontiers in genetics · 2023Article
- HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences.GigaScience · 2022Article
- flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Computational methods for chromosome-scale haplotype reconstruction.Genome biology · 2021Review
- Estimation of Molecular Pairwise Relatedness in Autopolyploid Crops.G3 (Bethesda, Md.) · 2020Article
- Haplotype threading: accurate polyploid phasing from long reads.Genome biology · 2020Article
- ComHapDet: a spatial community detection algorithm for haplotype assembly.BMC genomics · 2020Article
- Hap10: reconstructing accurate and long polyploid haplotypes using linked reads.BMC bioinformatics · 2020Article
- Ranbow: A fast and accurate method for polyploid haplotype reconstruction.PLoS computational biology · 2020Article
- Minimum error correction-based haplotype assembly: Considerations for long read data.PloS one · 2020Article
- Haplotype assembly of autotetraploid potato using integer linear programing.Bioinformatics (Oxford, England) · 2019Article
- A polyploid admixed origin of beer yeasts derived from European and Asian wine populations.PLoS biology · 2019Article
- A graph-based algorithm for estimating clonal haplotypes of tumor sample from sequencing data.BMC medical genomics · 2019Article
- Long-read sequence and assembly of segmental duplications.Nature methods · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe goal of haplotype assembly is to infer haplotypes of an individual from a mixture of sequenced chromosome fragments. Limited lengths of paired-end sequencing reads and inserts render haplotype assembly computationally challenging; in fact, most of the problem formulations are known to be NP-hard. Dimensions (and, therefore, difficulty) of the haplotype assembly problems keep increasing as the sequencing technology advances and the length of reads and inserts grow. The computational challenges are even more pronounced in the case of polyploid haplotypes, whose assembly is considerably more difficult than in the case of diploids. Fast, accurate, and scalable methods for haplotype assembly of diploid and polyploid organisms are needed.
resultsWe develop a novel framework for diploid/polyploid haplotype assembly from high-throughput sequencing data. The method formulates the haplotype assembly problem as a semi-definite program and exploits its special structure - namely, the low rank of the underlying solution - to solve it rapidly and with high accuracy. The developed framework is applicable to both diploid and polyploid species. The code for SDhaP is freely available at https://sourceforge.net/projects/sdhap .
conclusionExtensive benchmarking tests on both real and simulated data show that the proposed algorithms outperform several well-known haplotype assembly methods in terms of either accuracy or speed or both. Useful recommendations for coverages needed to achieve near-optimal solutions are also provided.
Indexed as
Identifiers
What OpenQuestion holds
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.