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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
...in length with a ≤1% error rate. High-quality long reads have been used to accurately assemble s (Kolmogorov et al. 2019; Nurk et al. 2020; Ekim et al. 2021; Bankevich et al. 2022), complete the human (Nurk et al. 2022), accurately detect small variants in challenging genomic regions (Olson et al. 2022...
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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
...et al. 2020). The emergence of long high-fidelity (HiFi) PacBio reads has, once again, revolutionized the field of assembly (Wenger et al. 2019; Logsdon et al. 2021) and resulted in some of the most contiguous assemblies to date (Nurk et al. 2020, 2022; Cheng et al. 2021).The emergence of “complete...
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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
...and evolution in muroid rodents. Mol Biol Evol 37: 3453–3468. doi:10.1093/molbev/msaa175 ↵Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. 2020. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...reads produced by deep sequencing with state-of-the-art Nanopore (10.4 flow cells, 200× coverage) and PacBio (HiFi 50×). The same exons are accurately assembled using Illumina 67× coverage. We find that these missing exons are consistently located near simple satellite sequences, in which sequencing...
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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
....MethodsThe original Verkko pipeline consisted of six main steps, with module dependencies given in parentheses: homopolymer compression and correction of LA reads (HiCanu) (Nurk et al. 2020), LA multiplex De Bruijn graph construction (MBG) (Rautiainen and Marschall 2021), alignment of UL reads to the LA graph (Graph...
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Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore...
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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: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...RAmbler, hifiasm, LJA, HiCANU, and Verkko on the subset of HiFi reads mapped to these regions. SDA was excluded because it “is no longer maintained and should not be used … assembly tools like Flye, HiCanu, and hifiasm outperform any results previously possible with SDA” (quote from https...
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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
...-quality reconstructions of nonhuman s. We discuss training data in Methods.In addition to the contiguity of the assemblies, we evaluated their gene completeness, QVs, and misassemblies. While the percentage of duplicated genes on CHM13 and A. thaliana is similar for GNNome, hifiasm, and Verkko, for HiCanu...
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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...on the application, sequencing depth, sequencing platform, and type of sequenced. For example, for short-read assembly, the choice of k might optimize the number of recognizable genomic k-mers (Chikhi and Medvedev 2014), but for high-fidelity long-read sequencing data, much higher values of k can be used, because...
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