ArticleGenome research2024
Phased nanopore assembly with Shasta and modular graph phasing with GFAse.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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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.
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Who cites it
23 citing papers in PubMed.
- Automatic generation of model sequences for complex regions in assembly graphs with TTT.Cell genomics · 2026Article
- Evolution of compound eye cell types shapes visual behaviors acrossbioRxiv : the preprint server for biology · 2026Article
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- Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches.Nature ecology & evolution · 2026Article
- Automatic Generation of Model Sequences for Complex Regions in Assembly Graphs.bioRxiv : the preprint server for biology · 2026Article
- A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie.G3 (Bethesda, Md.) · 2026Article
- Efficient near telomere-to-telomere assembly of Nanopore Simplex reads.bioRxiv : the preprint server for biology · 2025Article
- A non-invasive method to genotype cephalopod sex by quantitative PCR.bioRxiv : the preprint server for biology · 2025Article
- Natural Habitat and Wild Behaviors of the Dwarf Cuttlefish,Ecology and evolution · 2025Article
- Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding.Genome research · 2025Article
- Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation.bioRxiv : the preprint server for biology · 2024Article
- Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data.Bioinformatics (Oxford, England) · 2024Article
- Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.Genome research · 2024Article
- Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing.Genome biology · 2024Article
- Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing.bioRxiv : the preprint server for biology · 2024Article
- Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph.Nature methods · 2024Article
- Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall.Genome research · 2023Article
- Genome assembly in the telomere-to-telomere era.ArXiv · 2023Article
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23 authors.
Funding
Abstract
Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of ONT PromethION sequencing, including those using proximity ligation, and show that newer, higher accuracy ONT reads substantially improve assembly quality.
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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.