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Method: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic
- Jim Shaw and
- Yun William Yu
Genome Res. July 2023 33: 1175-1187; Published in Advance March 29, 2023, doi:10.1101/gr.277637.122
...with k-mer seeds is a powerful heuristic technique for sequence alignment used by modern sequence aligners. Although effective in practice for both runtime and accuracy, theoretical guarantees on the resulting alignment do not exist for seed-chain-extend. In this work, we give the first rigorous bounds...
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Erratum: Erratum: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 660; doi:10.1101/gr.281963.126
...Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.281963.126 ;36/3/660 ;gr.281963.126 660 gr.281963.126 Erratum Erratum Errata Erratum Erratum Groza Cristian Ge Bing Cheung Warren A. Pastinen Tomi Bourque Guillaume 3...
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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
...information has opened ample opportunities for the addition of extrinsic evidence (Guigo et al. 2006; Coghlan et al. 2008; Goodswen et al. 2012; Scalzitti et al. 2020). This addition proved to be critically important for increasing gene-prediction accuracy in large plant and animal s having low gene density...
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Method: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses
- Benjamin Kaminow,
- Sara Ballouz,
- Jesse Gillis,
- and Alexander Dobin
Genome Res. April 2022 32: 738-749; Published in Advance March 7, 2022, doi:10.1101/gr.275613.121
...genomic analyses. However, in its present form, it does not adequately represent the vast genetic diversity of the human population. In this study, we explored the consensus as a potential successor of the current reference and assessed its effect on the accuracy of RNA-seq read alignment. To find...
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Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
- Alexander Zee,
- Dori Z.Q. Deng,
- Matthew Adams,
- Kayla D. Schimke,
- Russell Corbett-Detig,
- Shelbi L. Russell,
- Xuan Zhang,
- Robert J. Schmitz,
- and Christopher Vollmers
Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
...-throughput sequencers. However, standard per-base sequencing accuracy of the newest base-calling software guppy5 is only ∼96% and is dominated by insertion and deletion errors, which are almost absent in Illumina data. Furthermore, ONT MinION's sequencing accuracy declines with shorter reads (Thirunavukarasu et al...
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Research: Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
- Gregor Diensthuber,
- Leszek P. Pryszcz,
- Laia Llovera,
- Morghan C. Lucas,
- Anna Delgado-Tejedor,
- Sonia Cruciani,
- Jean-Yves Roignant,
- Oguzhan Begik,
- and Eva Maria Novoa
Genome Res. November 2024 34: 1865-1877; Published in Advance September 13, 2024, doi:10.1101/gr.278849.123
....ResultsRNA basecalling model choice affects both per-read accuracy and RNA modification “errors”To test whether the use of alternative basecalling models could enhance the detection of RNA modifications using alignment feature-based tools, we trained novel RNA basecalling models using two different approaches...
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Method: Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy
- Moonseong Jeong,
- Ali Pazokitoroudi,
- Zhengtong Liu,
- and Sriram Sankararaman
Genome Res. September 2024 34: 1286-1293; Published in Advance July 22, 2024, doi:10.1101/gr.279207.124
...the development of methods that only require summary statistics. Although the availability of publicly accessible summary statistics makes them widely applicable, these methods lack the accuracy of methods that utilize individual genotypes. Here we present a SUMmary-statistics-based Randomized Haseman...
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Method: Whole-genome bisulfite sequencing with improved accuracy and cost
- Masako Suzuki,
- Will Liao,
- Frank Wos,
- Andrew D. Johnston,
- Justin DeGrazia,
- Jennifer Ishii,
- Toby Bloom,
- Michael C. Zody,
- Soren Germer,
- and John M. Greally
Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
...Whole- bisulfite sequencing with improved accuracy and cost Masako Suzuki1,3, Will Liao2,3, Frank Wos2,3, Andrew D. Johnston1, Justin DeGrazia2, Jennifer Ishii2, Toby Bloom2, Michael C. Zody2, Soren Germer2 and John M. Greally1 1Center for Epigenomics and Department of Genetics, Albert Einstein...
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Method: UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
- Tom Smith,
- Andreas Heger,
- and Ian Sudbery
Genome Res. March 2017 27: 491-499; Published in Advance January 18, 2017, doi:10.1101/gr.209601.116
...-seq and iCLIP (König et al. 2010), UMIs may be applied to almost any sequencing method in which confident identification of PCR duplicates by alignment coordinates alone is not possible and/or an accurate quantification is required, including ChIP-exo (He et al. 2015), DNA-seq karyotyping (Karlsson et al...
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ERRATUM: Erratum Genome Res. September 2008 18: 1544

...weight of all its edges (p. 1322) should be: i=1 logs#2;xi|#1;i = i=1 w#2;xi,#1;i + i=1 logs#2;xi|#2;#3;. Compelled edges exist only in general models, and finding the maximal score is NP-hard. The authors apologize for any confusion this may have caused. Erratum 1544 Genome Research www..org 18...

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