Evidence map›Paper›PMID 42561952›Full record

ArticleCell genomics2026

Automatic generation of model sequences for complex regions in assembly graphs with TTT.

Dmitry Antipov, Ying Chen, Marco Sollitto, Adam M Phillippy, Giulio Formenti, Sergey Koren

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 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

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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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

6 authors.

Dmitry AntipovGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institute of Health, Bethesda, MD 20892, USA.
Ying ChenThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Marco SollittoThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA; Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy.
Adam M PhillippyGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institute of Health, Bethesda, MD 20892, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: aphillippy@jhu.edu.
Giulio FormentiThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA. Electronic address: gformenti@rockefeller.edu.
Sergey KorenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institute of Health, Bethesda, MD 20892, USA. Electronic address: sergekoren@gmail.com.

Funding

Gfastar: a C++ library and a tool suite to aid Telomere-to-Telomere genome assemblyR03HG013362 · NHGRI · ROCKEFELLER UNIVERSITY · PI FORMENTI, GIULIO · 2024 to 2024
$170k
NHGRI NIH HHS R03 HG013362
6 · The paper itself

Abstract

Recent developments have enabled the automated assembly of vertebrate chromosomes from telomere to telomere. However, for long, highly similar repeats, genome assemblers may leave tangles in the assembly graph and gaps in the assembly. In recently published genomes, such gaps are closed by manual graph curation, a process that is labor intensive, error prone, and sometimes infeasible. Consequently, important genomic regions may be misassembled or omitted. Here, we present the trivial tangle traverser (TTT) algorithm that finds optimized resolutions of assembly graph tangles. TTT uses depth of coverage and read-to-graph alignment information in a two-stage process to estimate sequence multiplicities and identify traversals that are consistent with the underlying data. We evaluate TTT traversals on the HG002 human reference genome, compare TTT with a state-of-the-art assembler on the giraffe T2T assembly, and demonstrate its use to characterize a previously unassembled amplified p21-activated serine/threonine kinase 3-like (PAK3L) gene array in the zebra finch genome.

Indexed as

AlgorithmsModels, GeneticSequence Analysis, DNAAnimalsFinchesGenomeGenome, HumanGenomicsHumansp21-Activated KinasesTelomerep21-Activated Kinasesampliconic gene arraysEulerian pathgap closinggenome assemblymixed-integer linear programmingPAK3Taeniopygia guttatatelomere-to-telomere assemblyzebra finch

Identifiers

PMID42561952
PMCPMC13477013

What OpenQuestion holds

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Registered trials

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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.