ArticleNature biotechnology2023
Telomere-to-telomere assembly of diploid chromosomes with Verkko.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 322 papers.
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Who cites it
322 citing papers in PubMed.
- An Icelandic pangenome reference.Nature · 2026Article
- COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs.Genome biology · 2026Article
- De Novo Assembly of the Trypanosoma congolense Genome Reveals an Organization Influenced by Antigenic Variation but Distinct from Trypanosoma brucei.Genome biology and evolution · 2026Article
- ONT-only genome assembly of a Korean male individual using a semen sample.Genes & genomics · 2026Article
- The telomere-to-telomere gap-free reference genome and DNA methylome unveil epigenetic regulation of proanthocyanidin biosynthesis during apricot fruit development.The Plant journal : for cell and molecular biology · 2026Article
- Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.PLoS computational biology · 2026Article
- Telomere-to-telomere genome ofHorticulture research · 2026Article
- Automatic generation of model sequences for complex regions in assembly graphs with TTT.Cell genomics · 2026Article
- Phased T2T horse and donkey assemblies from a mule reveal peculiar equid centromere evolution.Cell genomics · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
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- A complete genome for the common marmoset.Cell · 2026Article
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- Long-term surveillance reveals hybridization by nuclear reassortment and intercontinental spread as major evolutionary drivers in wheat yellow rust.The New phytologist · 2026Article
- A pangenome of tetraploid wheat reveals the genetic architecture underlying domestication and genomic diversity for breeding.Nature genetics · 2026Article
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- Chromosome-scale genome of European anchovy (Engraulis encrasicolus L., 1758) and comparative genomics uncover clupeid-specific immune gene expansions.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Artificial intelligence in plant salt stress research: from predictive models to multi-omics integration.Journal of experimental botany · 2026Review
262 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on manual integration of ultra-long Oxford Nanopore sequencing reads with a high-resolution assembly graph built from long, accurate PacBio high-fidelity reads. We have improved and automated this strategy in Verkko, an iterative, graph-based pipeline for assembling complete, diploid genomes. Verkko begins with a multiplex de Bruijn graph built from long, accurate reads and progressively simplifies this graph by integrating ultra-long reads and haplotype-specific markers. The result is a phased, diploid assembly of both haplotypes, with many chromosomes automatically assembled from telomere to telomere. Running Verkko on the HG002 human genome resulted in 20 of 46 diploid chromosomes assembled without gaps at 99.9997% accuracy. The complete assembly of diploid genomes is a critical step towards the construction of comprehensive pangenome databases and chromosome-scale comparative genomics.
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