ArticleGenome biology2020
Haplotype threading: accurate polyploid phasing from long reads.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
- nTChap: an accurate method for polyploid haplotype reconstruction.BMC genomics · 2026Article
- SyFi: generating and using sequence fingerprints to distinguish SynCom isolates.Microbial genomics · 2025Article
- Long-range PCRs and next-generation sequencing to detect cytomegalovirus drug resistance-associated mutations.Antimicrobial agents and chemotherapy · 2025Article
- Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects.Molecular ecology · 2025Article
- Review
- HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.International journal of molecular sciences · 2025Article
- The phased pan-genome of tetraploid European potato.Nature · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points.Nature protocols · 2025Review
- Direct inference of haplotypes from sequencing data.Bioinformatics advances · 2025Article
- Current Progress in Phased Genome Assembly from Long-Read DNA Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Harpy: a pipeline for processing haplotagging linked-read data.Bioinformatics advances · 2025Article
- Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat.Communications biology · 2024Article
- Evolution of Plant Genome Size and Composition.Genomics, proteomics & bioinformatics · 2024Review
- Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing.Nature methods · 2024Article
- GCphase: an SNP phasing method using a graph partition and error correction algorithm.BMC bioinformatics · 2024Article
- Floria: fast and accurate strain haplotyping in metagenomes.Bioinformatics (Oxford, England) · 2024Article
- The Promise of Inferring the Past Using the Ancestral Recombination Graph.Genome biology and evolution · 2024Article
- Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data.Genome biology · 2024Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WHATSHAP POLYPHASE, a novel two-stage approach that addresses these challenges by (i) clustering reads and (ii) threading the haplotypes through the clusters. Our method outperforms the state-of-the-art in terms of phasing quality. Using a real tetraploid potato dataset, we demonstrate how to assemble local genomic regions of interest at the haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap.
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