Searching journal content for articles similar to Carvalho et al. 26 (12): 1710.

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  1. Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
    • Romain Derelle,
    • Johanna von Wachsmann,
    • Tommi Mäklin,
    • Joel Hellewell,
    • Timothy Russell,
    • Ajit Lalvani,
    • Leonid Chindelevitch,
    • Nicholas J. Croucher,
    • Simon R. Harris,
    • and John A. Lees
    Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
    ...was first introduced through the kSNP program (Gardner and Hall 2013; Gardner et al. 2015; Hall and Nisbet 2023). We previously implemented an enhanced version of this approach in the SKA (“split k-mer analysis”) software, hereafter referred to as SKA1. SKA1 offered improvements in efficiency...
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  2. Method: Telomere-to-telomere assembly by preserving contained reads
    • Sudhanva Shyam Kamath,
    • Mehak Bindra,
    • Debnath Pal,
    • and Chirag Jain
    Genome Res. November 2024 34: 1908-1918; Published in Advance October 15, 2024, doi:10.1101/gr.279311.124
    ...of a sequencing experiment as a multiset of reads, where each read is identified by its haplotype of origin, length, and stop position. The user provides a read-length distribution and sequencing depths of two haplotypes as input. Accordingly, the set of valid sequencing outputs includes all possible multisets...
  3. Method: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
    • Sergey Koren,
    • Brian P. Walenz,
    • Konstantin Berlin,
    • Jason R. Miller,
    • Nicholas H. Bergman,
    • and Adam M. Phillippy
    Genome Res. May 2017 27: 722-736; Published in Advance March 15, 2017, doi:10.1101/gr.215087.116
    ...more continuous than prior versions. Adaptive MinHash k-mer weighting Optimal handling of repeats is a challenge, because in addition to fragmenting assemblies, repeats also cause computational bottlenecks during overlapping. Read overlapping typically proceeds in two stages: first building a list...
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  4. 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
    ...lengths for HiFi reads and thus connect solid k-mers surrounding “solid k-mer deserts”—long stretches of DNA without any solid k-mers. Together with rapidly improving chemistry, ONT reads might become a self-sufficient alternative for quality assessment of assembly.VerityMap has been designed primarily...
  5. Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
    • Sergey Nurk,
    • Brian P. Walenz,
    • Arang Rhie,
    • Mitchell R. Vollger,
    • Glennis A. Logsdon,
    • Robert Grothe,
    • Karen H. Miga,
    • Evan E. Eichler,
    • Adam M. Phillippy,
    • and Sergey Koren
    Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
    ...and as the Chromosome X sequence itself is not error free, this likely represents a lower bound on the percentage of error-free reads. To extend beyond Chr X, we also estimated read accuracy using k-mers from short-read data for all human s and found correction improved read accuracy across all data sets (Supplemental...
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  6. 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
    ...and accurate s. Additionally, the underrepresented Y-linked exons provide a valuable benchmark for refining those sequencing technologies while improving the assembly of the highly heterochromatic and often neglected Drosophila Y Chromosome.Long-read sequencing (LRS) technologies Pacific Biosciences (Pac...
  7. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ...schemes such as pseKNC, pseDNC, and DAC are unsuitable for the 4mC site prediction task based on DL architecture based on computational efficiency and contribution to accuracy improvement. Ultimately, this study utilizes the remaining 14 feature encoding schemes—ENAC, Binary, NCP, EIIP, k-mer, CKSNAP, Pse...
    OPEN ACCESS ARTICLE
  8. Method: Highly accurate assembly polishing with DeepPolisher
    • Mira Mastoras,
    • Mobin Asri,
    • Lucas Brambrink,
    • Prajna Hebbar,
    • Alexey Kolesnikov,
    • Daniel E. Cook,
    • Maria Nattestad,
    • Julian Lucas,
    • Taylor S. Won,
    • Pi-Chuan Chang,
    • Andrew Carroll,
    • Benedict Paten,
    • Kishwar Shafin,
    • and and the Human Pangenome Reference Consortium
    Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
    ...methods generally report a quality value (QV), a log base 10–scaled measure of assembly error, with higher values indicating more accurate assemblies. We find that DeepPolisher improves the k-mer-based assembly QV by 1.8, equivalent to a 34% reduction in errors, which is approximately consistent...
  9. 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
    ...are extracted from each read using a 64-bit rolling hash and minimizer parameters of k-mer length k = 425 and window size w = 19. The sequences of the minimizers are ignored, and only the hash value and start and end positions within the read are stored. A maximum copy count (default, 1000) is used to filter...
    OPEN ACCESS ARTICLE
  10. 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
    ...the generalization capability of our model to the full human CHM13—even though not all the chromosomes were seen in either training or validation, our model consistently performs well. The chromosomes chosen for training were sampled 15 times each to produce samples of reads, which resulted in 15 hifiasm...
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