ArticleGenome biology2024
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- Graph statistics theory of individualized quantitative genetics under haplotype-resolved genome assembly.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Distinct mechanisms of CNV formation at the human 15q13.3 locus.bioRxiv : the preprint server for biology · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Article
- Article
- Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic Disorders.Diagnostics (Basel, Switzerland) · 2025Review
- Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding.Genome research · 2025Article
- Article
- Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing.Genome biology · 2024Article
- Complex genetic variation in nearly complete human genomes.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
8 authors.
Funding
Abstract
Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haplotype-collapsed assembly. Here, we present Graphasing, a workflow which synthesizes the global phase signal of Strand-seq with assembly graph topology to produce chromosome-scale de novo haplotypes for diploid genomes. Graphasing readily integrates with any assembly workflow that both outputs an assembly graph and has a haplotype assembly mode. Graphasing performs comparably to trio phasing in contiguity, phasing accuracy, and assembly quality, outperforms Hi-C in phasing accuracy, and generates human assemblies with over 18 chromosome-spanning haplotypes.
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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 OpenQuestion graph.