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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
..., Haikou, Hainan 571101, China Corresponding authors: sergey.koren@nih.gov, adam.phillippy@nih.govAbstractThe combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human...
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Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
- Samuel T. Horsfield,
- Basil C.T. Fok,
- Yuhan Fu,
- Paul Turner,
- John A. Lees,
- and Nicholas J. Croucher
Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
...and portable serotyping method that overcomes these challenges, we employed nanopore adaptive sampling (NAS), an on-sequencer enrichment method that selects for target DNA in real-time, for direct detection of S. pneumoniae in complex samples. Whereas NAS targeting the whole S. pneumoniae was ineffective...
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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
....The application of long-read sequencing further reduces false-positive calls and enhances clinical interpretation. A study using nanopore sequencing reassessed SVs initially identified by Illumina in 669 cancer patients, confirming eight pathogenic or likely pathogenic SVs and resolving three additional variants...
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Method: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
- Ryan Lorig-Roach,
- Melissa Meredith,
- Jean Monlong,
- Miten Jain,
- Hugh E. Olsen,
- Brandy McNulty,
- David Porubsky,
- Tessa G. Montague,
- Julian K. Lucas,
- Chris Condon,
- Jordan M. Eizenga,
- Sissel Juul,
- Sean K. McKenzie,
- Sara E. Simmonds,
- Jimin Park,
- Mobin Asri,
- Sergey Koren,
- Evan E. Eichler,
- Richard Axel,
- Bruce Martin,
- Paolo Carnevali,
- Karen H. Miga,
- and Benedict Paten
Genome Res. March 2024 34: 454-468; Published in Advance April 16, 2024, doi:10.1101/gr.278268.123
...to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta assembler and a modular tool for extending phasing to the chromosome scale called...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...methods to effectively differentiate technology errors from rare but real molecules. For annotation, we must agree on the strategy to capture molecular variability while still defining reference annotations that are useful for the genomics community.Long-read sequencing (LRS) technologies, such as those...
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Method: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
- Alla Mikheenko,
- Andrey D. Prjibelski,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. April 2022 32: 726-737; Published in Advance March 17, 2022, doi:10.1101/gr.276405.121
...molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and long-read sequencing to sequence cDNA copies representing an individual RNA molecule on both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). We compare these long-read pairs in terms...
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Method: Robust 16S rRNA classification based on a compressed LCA index
- Omar Ahmed,
- Christina Boucher,
- and Ben Langmead
Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
...classifications using a compressed full-text index. Cliffy uses a novel compression scheme to reduce the size of the document array profiles (Ahmed et al. 2023a) by two orders of magnitude to make it practical for 16S rRNA classification. In addition, Cliffy incorporates strategies such as minimizer digestion...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...Oxford Nanopore Technologies, Oxford OX4 4DQ, United Kingdom ↵4 These authors contributed equally to this work. Corresponding authors: adam.phillippy@nih.gov, sergey.koren@nih.govAbstractThe Telomere-to-Telomere Consortium recently finished the first truly complete sequence of a human . To resolve...
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Method: Efficient taxa identification using a pangenome index
- Omar Ahmed,
- Massimiliano Rossi,
- Christina Boucher,
- and Ben Langmead
Genome Res. July 2023 33: 1069-1077; Published in Advance May 31, 2023, doi:10.1101/gr.277642.123
...of Engineering, University of Florida, Gainesville, Florida 32611, USA Corresponding author: oahmed6@jhu.edu, omaryfekry@gmail.comAbstractTools that classify sequencing reads against a database of reference sequences require efficient index data-structures. The r-index is a compressed full-text index...
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Method: Efficient mapping of accurate long reads in minimizer space with mapquik
- Bariş Ekim,
- Kristoffer Sahlin,
- Paul Medvedev,
- Bonnie Berger,
- and Rayan Chikhi
Genome Res. July 2023 33: 1188-1197; Published in Advance June 30, 2023, doi:10.1101/gr.277679.123
...-and-extend strategy. Specifically, seeds are short k-mer minimizers, namely, sequences of length k that are lexicographically minimal within a window of w consecutive k-mers. The extension step is performed using an optimized implementation of the Needleman–Wunsch algorithm (Needleman and Wunsch 1970) with an affine...
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