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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...significantly improved bacterial pathogen genomics, diagnostics, and epidemiology. Despite its high accuracy, short-read sequencing struggles with the complete reconstruction and assembly of extrachromosomal elements such as plasmids. Long-read sequencing with Oxford Nanopore Technologies (ONT) presents...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...1, Raony Cardenas1, Thyago Cardoso1, Luis F. Paulin2, Philippe Sanio2, Joseph Mafofo1, Haiguo Wu1, Val Zvereff1, Albarah El-Khani1, Fahed Al Marzooqi1, Tiago R. Magalhães1, Fritz J. Sedlazeck2,3,4 and Javier Quilez1 1M42, Abu Dhabi, United Arab Emirates; 2Human Genome Sequencing Center, Baylor...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...of class I loci (Daza-Vamenta et al. 2004; Fukami-Kobayashi et al. 2005; Shiina et al. 2006; Watanabe et al. 2007). Sequencing of an MHC class I B haplotype from a rhesus macaque bacterial artificial chromosome (BAC) library (CHORI-250) identified 19 distinct MHC-B genes (Daza-Vamenta et al. 2004; Shiina...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...modification, which plays important roles in genomic imprinting, X-Chromosome inactivation, and carcinogenesis (Smith and Meissner 2013). 5mC is classically detected using bisulfite sequencing (BS-seq), but BS-seq is destructive and reduces sequence complexity. BS-seq itself also cannot distinguish 5mC from 5...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...reads. This comprises 3.055 billion base pairs and addresses the previously unresolved 8% of the , including complex heterochromatic regions (Nurk et al. 2022). In 2023, the consortium finalized the complete Y Chromosome sequence (T2T-Y) from the HG002 donor (Rhie et al. 2023). The integration of T2T...
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Method: Fast and accurate mapping of long reads to complete genome assemblies with VerityMap
- Andrey V. Bzikadze,
- Alla Mikheenko,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2107-2118; Published in Advance November 15, 2022, doi:10.1101/gr.276871.122
...-read sequencing have enabled the telomere-to-telomere (complete) assembly of a human and are now contributing to the haplotype-resolved complete assemblies of multiple human s. Because the accuracy of read mapping tools deteriorates in highly repetitive regions, there is a need to develop accurate, error...
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Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
...are an integral component of the biological information about an organism; thus, the more complete the , the more informative it is. Historically, bacterial and archaeal s were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
..._Celera) was released in 2006 and included sequence from both the Brown Norway and outbred Sprague Dawley strains. Assembly employed a hybrid approach combining whole- shotgun sequencing with bacterial artificial chromosome clone sequencing, resulting in highly fragmented assemblies. Rnor_6.0 sought to reduce...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high-quality sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short...
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Method: MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome
- John R. Tyson,
- Nigel J. O'Neil,
- Miten Jain,
- Hugh E. Olsen,
- Philip Hieter,
- and Terrance P. Snutch
Genome Res. February 2018 28: 266-274; Published in Advance December 22, 2017, doi:10.1101/gr.221184.117
...improved by sequencing ultra-long DNA fragments (100–1000 kb), which are being made possible by the development of DNA extraction techniques and library construction protocols that reduce shearing of genomic DNA (Jain et al. 2017). Such ultra-long-read sequencing could truly complete the C. elegans...
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