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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
...lengths that exceed typical fragment lengths. ScatTR outperforms state-of-the-art methods for larger TRs and longer motifs up to 50 bp. Unlike classification-based approaches, ScatTR's model does not rely on directly counting repeat units within read sequences, allowing it to accommodate longer motifs...
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Method: Geometric deep learning framework for de novo genome assembly
- Lovro Vrček,
- Xavier Bresson,
- Thomas Laurent,
- Martin Schmitz,
- Kenji Kawaguchi,
- and Mile Šikić
Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
...novo assembler is identifying paths in assembly graphs that correspond to the reconstructed genomic sequences. The existing algorithmic methods struggle with this, primarily due to repetitive regions causing complex graph tangles, leading to fragmented assemblies. Here, we introduce GNNome, a framework...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
.../AMP) guidelines to classify genetic variants into five categories: pathogenic, likely pathogenic, benign, likely benign, and variant(s) of uncertain significance (VUS) (Richards et al. 2015). Whereas the first four classifications could be useful in interpreting rare variants that are found in genes that have...
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Method: Graph-based self-supervised learning for repeat detection in metagenomic assembly
- Ali Azizpour,
- Advait Balaji,
- Todd J. Treangen,
- and Santiago Segarra
Genome Res. September 2024 34: 1468-1476; Published in Advance July 19, 2024, doi:10.1101/gr.279136.124
...in red.Previous studies have employed prespecified graph features in combination with machine learning techniques to address the challenge of detecting repeats, treating it as a node classification problem (Ghurye and Pop 2016; Ghurye et al. 2019). In this context, the nodes of the graph represent DNA...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...Chromosome-level sub-aware de novo assembly provides insight into Saccharomyces bayanus divergence after hybridization Cory Gardner1,2,5, Junhao Chen3,5, Christina Hadfield2, Zhaolian Lu3, David Debruin2, Yu Zhan3, Maureen J. Donlin2,4, Tae-Hyuk Ahn1,2 and Zhenguo Lin2,3 1Department of Computer...
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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...are found only in one strand but not the other, showing a strand-specific bias. Leveraging this discovery, we developed Hammerhead, a pioneering pipeline designed for de novo methylation discovery that circumvents the necessity of raw signal inference and a methylation-free control. The majority (14 out...
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Research: Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
- John S. Sproul,
- Scott Hotaling,
- Jacqueline Heckenhauer,
- Ashlyn Powell,
- Dez Marshall,
- Amanda M. Larracuente,
- Joanna L. Kelley,
- Steffen U. Pauls,
- and Paul B. Frandsen
Genome Res. October 2023 33: 1708-1717; Published in Advance September 22, 2023, doi:10.1101/gr.277387.122
...abundance followed by LINEs, LTRs, and DNA transposons all as a percentage of the overall assembly. Totals for DNA transposons reported include TIR, Crypton, and Helitron/Polinton elements, reflecting the classification scheme of RepeatMasker, although the large majority in all cases are TIR (for a finer...
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Resource: Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
- Wenjuan Yu,
- Haohui Luo,
- Jinbao Yang,
- Shengchen Zhang,
- Heling Jiang,
- Xianjia Zhao,
- Xingqi Hui,
- Da Sun,
- Liang Li,
- Xiu-qing Wei,
- Stefano Lonardi,
- and Weihua Pan
Genome Res. February 2024 34: 326-340; Published in Advance March 1, 2024, doi:10.1101/gr.278232.123
...Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic s and metas Wenjuan Yu1,6, Haohui Luo1,6, Jinbao Yang1,5,6, Shengchen Zhang1,5,6, Heling Jiang1,6, Xianjia Zhao1,4, Xingqi Hui1,4, Da Sun1, Liang Li2, Xiu-qing Wei2, Stefano Lonardi3 and Weihua Pan1 1Shenzhen Branch...
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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
...The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal Young-Lim Lee1,2, Aniek C. Bouwman2, Chad Harland1,3, Mirte Bosse2, Gabriel Costa Monteiro Moreira1, Roel F. Veerkamp2, Erik Mullaart4, Nadine Cambisano5, Martien A...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...-read sequencing technology that has been applied reliably detects only single-nucleotide mutations (SNMs) and short insertions and deletions (indels), and little is known about the rates at which SMs occur de novo.SMs include larger indels (often defined as those >50 bp), duplications, transposable element (TE...
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