ArticlePLoS computational biology2020
Ranbow: A fast and accurate method for polyploid haplotype reconstruction.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives.Plant communications · 2022Pooled it
- Genome-wide analysis of FATA associated with drought tolerance in tetraploid potato (Frontiers in plant science · 2026Article
- Genetic linkage mapping in Megathyrsus maximus (Jacq.) with multiple dosage markers.G3 (Bethesda, Md.) · 2025Article
- Evolution of Plant Genome Size and Composition.Genomics, proteomics & bioinformatics · 2024Review
- DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering.Briefings in bioinformatics · 2024Article
- Haplotype based testing for a better understanding of the selective architecture.BMC bioinformatics · 2023Article
- From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).Briefings in bioinformatics · 2023Article
- Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences.Systematic biology · 2023Article
- Recent Advances in Assembly of Complex Plant Genomes.Genomics, proteomics & bioinformatics · 2023Review
- XHap: haplotype assembly using long-distance read correlations learned by transformers.Bioinformatics advances · 2023Article
- HAT: haplotype assembly tool using short and error-prone long reads.Bioinformatics (Oxford, England) · 2022Article
- Genetic polyploid phasing from low-depth progeny samples.iScience · 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
- Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression.PLoS computational biology · 2021Article
- nPhase: an accurate and contiguous phasing method for polyploids.Genome biology · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reconstructing haplotypes from sequencing data is one of the major challenges in genetics. Haplotypes play a crucial role in many analyses, including genome-wide association studies and population genetics. Haplotype reconstruction becomes more difficult for higher numbers of homologous chromosomes, as it is often the case for polyploid plants. This complexity is compounded further by higher heterozygosity, which denotes the frequent presence of variants between haplotypes. We have designed Ranbow, a new tool for haplotype reconstruction of polyploid genome from short read sequencing data. Ranbow integrates all types of small variants in bi- and multi-allelic sites to reconstruct haplotypes. To evaluate Ranbow and currently available competing methods on real data, we have created and released a real gold standard dataset from sweet potato sequencing data. Our evaluations on real and simulated data clearly show Ranbow's superior performance in terms of accuracy, haplotype length, memory usage, and running time. Specifically, Ranbow is one order of magnitude faster than the next best method. The efficiency and accuracy of Ranbow makes whole genome haplotype reconstruction of complex genome with higher ploidy feasible.
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