ArticleGenome biology2021
nPhase: an accurate and contiguous phasing method for polyploids.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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Who cites it
19 citing papers in PubMed.
- Genomic Evidence of Early-Diverging Domesticated Lineages in Norwegian Farmhouse Yeast.Genome biology and evolution · 2026Article
- BacPhase: Long-insert paired-end sequencing for bin marker construction and genome phasing.aBIOTECH · 2026Article
- nTChap: an accurate method for polyploid haplotype reconstruction.BMC genomics · 2026Article
- Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery.bioRxiv : the preprint server for biology · 2025Article
- Phased chromosome-level assembly provides insight into the genome architecture of hexaploid sweetpotato.Nature plants · 2025Article
- Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes.Molecular ecology resources · 2025Article
- The genome assembly of the farmed European whitefish Coregonus lavaretus L. from the Finnish selective breeding programme.BMC genomic data · 2025Article
- Current Progress in Phased Genome Assembly from Long-Read DNA Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Evolution of Plant Genome Size and Composition.Genomics, proteomics & bioinformatics · 2024Review
- Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose.Nature plants · 2024Article
- European farmhouse brewing yeasts form a distinct genetic group.Applied microbiology and biotechnology · 2024Article
- Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors.PeerJ · 2024Article
- Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae.Nature genetics · 2023Article
- Loss of Heterozygosity and Its Importance in Evolution.Journal of molecular evolution · 2023Review
- 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
- Unlocking the functional potential of polyploid yeasts.Nature communications · 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
- Different trajectories of polyploidization shape the genomic landscape of theGenome research · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy ( https://github.com/OmarOakheart/nPhase ). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids.
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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 Socratic graph.