ArticleGenome research2025
Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding.
Article in Genome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
- Automatic generation of model sequences for complex regions in assembly graphs with TTT.Cell genomics · 2026Article
- Telomere-to-telomere genome assembly and a pangenome for the rat.Cell genomics · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
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- Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.Genome research · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
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- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Haplotype-aware long-read error correction.Algorithms for molecular biology : AMB · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.bioRxiv : the preprint server for biology · 2026Article
- Rapid centromere turnover and the adaptive radiation of lemurs.bioRxiv : the preprint server for biology · 2026Article
- Haplotype-resolved genome assemblies of BJ and IMR-90 human fibroblast cell lines reveal extensive structural variation and enable reanalysis of historical sequencing data.Nucleic acids research · 2026Article
- Sex chromosome identification and genome curation from a single individual with SCINKD.Molecular biology and evolution · 2026Article
- Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes.bioRxiv : the preprint server for biology · 2026Article
- A Complete Genome for the Common Marmoset.bioRxiv : the preprint server for biology · 2026Article
- The complete genome of the KOLF2.1J reference iPSC line.bioRxiv : the preprint server for biology · 2026Article
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7 authors.
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Abstract
The Telomere-to-Telomere Consortium recently finished the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on the semimanual combination of long, accurate Pacific Biosciences (PacBio) HiFi and ultralong Oxford Nanopore Technologies sequencing reads. The Verkko assembler later automated this process, achieving complete assemblies for approximately half of the chromosomes in a diploid human genome. However, the first version of Verkko was computationally expensive and could not resolve all regions of a typical human genome. Here we present Verkko2, which implements a more efficient read correction algorithm, improves repeat resolution and gap closing, introduces proximity-ligation-based haplotype phasing and scaffolding, and adds support for multiple long-read data types. These enhancements allow Verkko2 to assemble all regions of a diploid human genome, including the short arms of the acrocentric chromosomes and both sex chromosomes. Together, these changes increase the number of telomere-to-telomere scaffolds by twofold, reduce runtime by fourfold, and improve assembly correctness. On a panel of 19 human genomes, Verkko2 assembles an average of 39 of 46 complete chromosomes as scaffolds, with 21 of these assembled as gapless contigs. Together, these improvements enable telomere-to-telomere comparative genomics and pangenomics, at scale.
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