Evidence map›Paper›PMID 42561955›Full record

ArticleCell genomics2026

Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.

Juhyun Kim, Benjamin D Rosen, Sarah E Fumagalli, Kristen L Kuhn, Amy Long, Jeffrey J Schoenebeck, Heather Schwartz, Lan Wu-Cavener, Aleksey V Zimin, Douglas R Cavener and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
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  6. A Complete Genome for the Common Marmoset.bioRxiv : the preprint server for biology · 2026
    Article
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors.

Juhyun KimCenter for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Benjamin D RosenAnimal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA.
Sarah E FumagalliAnimal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA.
Kristen L KuhnMeat Animal Research Center, USDA-ARS, Clay Center, NE 68933, USA.
Amy LongCincinnati Zoo and Botanical Garden, Cincinnati, OH 45220, USA.
Jeffrey J SchoenebeckCenter for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Roslin Institute and Royal (Dick) School of Veterinary Studies, Midlothian EH25 9RG, UK.
Heather SchwartzNashville Zoo, Nashville, TN 37211, USA.
Lan Wu-CavenerDepartment of Biology, Pennsylvania State University, University Park, PA 16802, USA.
Aleksey V ZiminDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Douglas R CavenerDepartment of Biology, Pennsylvania State University, University Park, PA 16802, USA.
Timothy P L SmithMeat Animal Research Center, USDA-ARS, Clay Center, NE 68933, USA.
Adam M PhillippyCenter for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Departments of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Sergey KorenCenter for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Arang RhieCenter for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: arang.rhie@nih.gov.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

High-quality reference genomes are critical for studying the biology of the genome, but current methods often leave gaps and errors, especially in repetitive regions. These issues arise from challenges in genome graph curation and are not fully resolvable by standard polishing approaches. To address this, we developed Verkko-Fillet, a Python-based interactive framework for inspecting, editing, and refining genome assembly graphs. It integrates multiple data sources and provides tools for visualization, gap filling, and structural correction. Applied to a giraffe and the benchmark human genome, Verkko-Fillet improves a draft assembly (Q61.5) to a complete telomere-to-telomere genome (Q73.6), increasing both contiguity and accuracy. This work highlights the importance of graph-based curation for producing a finished, gapless genome assembly suitable for downstream analyses.

Indexed as

GenomeGenomicsSoftwareTelomereAnimalsHumansassembly graphcomplete genome assemblydiploid assemblygenome assembly curationgenome assembly refinementgiraffe referencegraph-based curationhaplotype-resolved assemblyreference genomesTelomere-to-Telomere (T2T) genome assembly

Identifiers

PMID42561955
PMCPMC13477062

What OpenQuestion holds

Textmetadata
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Registered trials

None linked

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.