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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
..., especially when their expansions are larger than the fragment sizes used in standard short-read sequencing. Here, we introduce ScatTR, a novel computational method that leverages a maximum likelihood framework to estimate the copy number of large TR expansions from short-read sequencing data. Scat...
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Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
...to switch to using pans, a collection of s, as the reference. In this paper, we introduce Moni-align, the first short-read pan aligner built on the r-index, a variation of the classical FM-index that can index collections of s in O(r)-space, where r is the number of runs in the Burrows–Wheeler transform...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...or duplication of segments of DNA. Amplification of segments of DNA sequence, a type of copy number variation (CNV), is an important source of rapid adaptive evolution. In the short term, gene amplification can result in increased gene expression, which provides a selective advantage facilitating adaptation...
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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...associated with breast cancer risk (Helgadottir et al. 2021) and somatic variation in relapsed pediatric acute lymphoblastic leukemia (Sayyab et al. 2021).In this study, we aim to evaluate the improvement of mapping short-read WGS data to the new T2T-CHM13 reference compared to the reference s...
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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
...that the Brown Norway strain reflected an outbred, diploid . This resulted in the application of methods to identify allelic variation and to separate reads representing presumed different haplotypes into an alternative pseudohaploid assembly. One consequence of applying this approach to a that is fully inbred...
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Method: Detecting differential copy number variation between groups of samples
- Craig B. Lowe,
- Nicelio Sanchez-Luege,
- Timothy R. Howes,
- Shannon D. Brady,
- Rhea R. Daugherty,
- Felicity C. Jones,
- Michael A. Bell,
- and David M. Kingsley
Genome Res. February 2018 28: 256-265; Published in Advance December 11, 2017, doi:10.1101/gr.206938.116
...for detecting copy number variation from short sequencing reads. Although these programs do not explicitly annotate CNVs that differentiate two groups of samples, they represent the types of current methods that might be used in such an analysis.View larger version: In this window In a new window Figure 3...
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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...they are often not included in studies of -wide variation.Because of their low cost, mature and reliable technology, and proven high accuracy reads, second or “next-generation” short-read sequencing technologies are still the main technology for most studies. Long-read sequencing techniques, such as Pacific...
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Research: Extensive variation in germline de novo mutations in Poecilia reticulata
- Yuying Lin,
- Iulia Darolti,
- Wouter van der Bijl,
- Jake Morris,
- and Judith E. Mank
Genome Res. August 2023 33: 1317-1324; Published in Advance July 13, 2023, doi:10.1101/gr.277936.123
...the short guppy generation time. Overall, our study shows remarkable variation in germline mutation rate and provides insights into rapid evolution of guppies.Mutations underlie much of the diversity of life on earth. Moreover, the timing, rate, and spectra of germline mutations are fundamental aspects...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...crossovers to occur at specific locations in organisms that lack a functional copy of PRDM9. To get preliminary information about potential mechanistic underpinnings of recombination rate variation in wood whites, we assessed if specific sequence motifs or gene categories were enriched in recombination...
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Research: Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
- Eric R. Lucas,
- Alistair Miles,
- Nicholas J. Harding,
- Chris S. Clarkson,
- Mara K.N. Lawniczak,
- Dominic P. Kwiatkowski,
- David Weetman,
- Martin J. Donnelly,
- and The Anopheles gambiae 1000 Genomes Consortium
Genome Res. August 2019 29: 1250-1261; Published in Advance July 25, 2019, doi:10.1101/gr.245795.118
...the impact of copy number variation when calculating these normalizing constants, we excluded windows from the calculation of mean read counts for which previous analyses of accessibility have found evidence for excessively high or low coverage or ambiguous alignment (windows with <90% accessible bases...
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