Evidence map›Paper›PMID 38529488›Full record

ArticlebioRxiv : the preprint server for biology2024

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.

Sergey Koren, Zhigui Bao, Andrea Guarracino, Shujun Ou, Sara Goodwin, Katharine M Jenike, Julian Lucas, Brandy McNulty, Jimin Park, Mikko Rautiainen and 13 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

23 authors.

Sergey KorenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-1472-8962
Zhigui BaoDepartment of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, BadenWürttemberg, Germany.ORCID 0000-0003-3601-460X
Andrea GuarracinoDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.ORCID 0000-0001-9744-131X
Shujun OuOhio State University, Columbus, OH, USA.ORCID 0000-0001-5938-7180
Sara GoodwinCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Katharine M JenikeDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.ORCID 0000-0002-7276-8110
Julian LucasUniversity of California Santa Cruz, Santa Cruz, CA, USA.
Brandy McNultyUniversity of California Santa Cruz, Santa Cruz, CA, USA.
Jimin ParkUniversity of California Santa Cruz, Santa Cruz, CA, USA.
Mikko RautiainenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Arang RhieGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-9809-8127
Dick RoelofsKeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands.
Harrie SchneidersKeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands.
Ilse VrijenhoekKeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands.
Koen NijbroekKeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands.
Doreen WareCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Michael C SchatzDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.ORCID 0000-0002-4118-4446
Erik GarrisonDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.ORCID 0000-0003-3821-631X
Sanwen HuangShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
W Richard McCombieCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Karen H MigaUniversity of California Santa Cruz, Santa Cruz, CA, USA.ORCID 0000-0001-9709-4565
Alexander H J WittenbergKeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands.ORCID 0000-0002-0482-2592
Adam M PhillippyGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-2983-8934

Funding

Single-Cell Biology Shared ResourceP30CA045508 · NCI · COLD SPRING HARBOR LABORATORY · PI David A Tuveson · 1987 to 2026
$118.9M
ELSI Administrative Supplement - Center for Human Reference Genome DiversityU01HG010971 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI EICHLER, EVAN, JARVIS, ERICH D · 2019 to 2023
$18.4M
Telomere-to-telomere assemblies of human genomesR01HG011274 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Karen Hayden Miga · 2020 to 2026
$4.5M
The Development and Optimization of Long-Read Sequencing Applications to Cancer Genomics in a Core SettingR50CA243890 · NCI · COLD SPRING HARBOR LABORATORY · PI GOODWIN, SARA · 2019 to 2025
$920k
NCI NIH HHS P30 CA045508NCI NIH HHS R50 CA243890NHGRI NIH HHS R01 HG011274NHGRI NIH HHS U01 HG010971
6 · The paper itself

Abstract

The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, "telomere-to-telomere" genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT "Duplex" sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely-studied genomes: human HG002,

Indexed as

duplex sequencingGenome assemblygenome sequencinghaplotype phasingLRS Special IssueOxford Nanoporesingle-molecule sequencingtelomere-to-telomere assembly

Identifiers

PMID38529488
PMCPMC10962732

What OpenQuestion holds

Textmetadata
LicenceCC0
Read underepoch 390

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.