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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
...v5.0.0) (Dolzhenko et al. 2017), and HLA (using HLA-LA v1.0.3) (Dilthey et al. 2019) using the CRAM and VCF outputs from ZBOLT. Summary statistics of alignment/variant calls and various logs of tools from ZBOLT are stored.ONTThe PromethION (P48) sequencing system generates raw signal data...
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Method: Enhancing nanopore adaptive sampling for PromethION using readfish at scale
- Rory Munro,
- Alexander Payne,
- Nadine Holmes,
- Chris Moore,
- Inswasti Cahyani,
- and Matthew Loose
Genome Res. April 2025 35: 877-885; Published in Advance January 30, 2025, doi:10.1101/gr.279329.124
...is fundamentally the same as that of readfish; however, it is deeply embedded in MinKNOW, making it hard to customize and inflexible in certain scenarios. For example, it does not offer the ability to alter genomic targets during sequencing.With the release of the PromethION, nanopore sequencing has grown...
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Method: A new compression strategy to reduce the size of nanopore sequencing data
- Kavindu Jayasooriya,
- Sasha P. Jenner,
- Pasindu Marasinghe,
- Udith Senanayake,
- Hassaan Saadat,
- David Taubman,
- Roshan Ragel,
- Hasindu Gamaarachchi,
- and Ira W. Deveson
Genome Res. July 2025 35: 1574-1582; Published in Advance May 15, 2025, doi:10.1101/gr.280090.124
...was observed previously with DNA data above (Fig. 4A). Similarly, 3 bits could be removed with no impact on RNA basecalling accuracy down to a 3-bit reduction, as measured on native human mRNA (UHRR-Prom; sequenced on a PromethION) and synthetic RNA controls (SIRV-Min; sequenced on a MinION) (Fig. 4B). We...
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Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
- Jesper Eisfeldt,
- Edward J. Higginbotham,
- Felix Lenner,
- Jennifer Howe,
- Bridget A. Fernandez,
- Anna Lindstrand,
- Stephen W. Scherer,
- and Lars Feuk
Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
...using microarray or short-read sequencing (GS), these methods frequently fail to characterize breakpoints at nucleotide resolution, requiring additional molecular methods for validation and fine-mapping. Here, we use Oxford Nanopore Technologies PromethION long-read GS to characterize complex genomic...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...the past decade. The median alignment identity has increased from 85% in 2014 (R9 ONT and chemistry) to 99.7%+ in 2023 (R10 Nanopore Duplex chemistry). Throughput has also increased to the point where sequencing a 30×+ is routinely achievable using a single PromethION flow cell (Kolmogorov et al. 2023...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
.... For some initial samples (see Supplemental Table S1), a yeast spike-in control was added to the libraries, as described in Choquet et al. (2023). Sequencing was performed for up to 72 h with FLO-MIN106D, FLO-PRO002, or FLO-PRO004RA flow cells on a MinION or a PromethION 2 Solo device (Oxford Nanopore...
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Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
- Leszek P. Pryszcz,
- Gregor Diensthuber,
- Laia Llovera,
- Rebeca Medina,
- Anna Delgado-Tejedor,
- Luca Cozzuto,
- Julia Ponomarenko,
- and Eva Maria Novoa
Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
...performance (computation time and CPU usage). The applicability of SeqTagger was tested across sequencing devices (MinION and PromethION), sequencing chemistries (SQK-RNA002 and SQK-RNA004), RNA biotypes (poly(A)+ and tRNA), and for extended sets of barcodes (up to 96 barcodes).ResultsDemultiplexing DRS...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
.... 2021; Cohen et al. 2022).Addressing these needs, we performed long-read sequencing with Oxford Nanopore Technologies (ONT) on 68 individuals from the undiagnosed disease network (UDN) with preexisting short-read sequence data to study the improvement in variant detection recall from SR-GS. Then, using...
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Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
- Wouter De Coster,
- Ida Höijer,
- Inge Bruggeman,
- Svenn D'Hert,
- Malin Melin,
- Adam Ameur,
- and Rosa Rademakers
Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
...version includes 1040 individuals of The 1000 Genomes Project cohort sequenced on the Oxford Nanopore Technologies PromethION. A comprehensive set of medically relevant tandem repeats has been genotyped using STRdust and LongTR to determine the tandem repeat length and sequence composition. Path...
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Method: 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,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
...-208-300). Library preparation was carried out using Oxford Nanopore Technologies’ Ligation Sequencing Kit V14 (SQK-LSK114). PromethION high duplex flow cells were provided by ONT for sequencing on the PromethION 48 sequencer. Three libraries were prepared per flow cell. Flow cells were washed using ONT's Flow Cell...

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