Searching journal content for articles similar to Özden et al. 32 (6): 1170.

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  1. 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
    .... Here, we present an encoder-only transformer model for assembly polishing called DeepPolisher, which predicts corrections to the underlying sequence using Pacific Biosciences (PacBio) HiFi read alignments to a diploid assembly. Our pipeline introduces a method, PHAsing Reads in Areas Of Homozygosity...
  2. Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
    • Susan M. Hiatt,
    • James M.J. Lawlor,
    • Lori H. Handley,
    • Donald R. Latner,
    • Zachary T. Bonnstetter,
    • Candice R. Finnila,
    • Michelle L. Thompson,
    • Lori Beth Boston,
    • Melissa Williams,
    • Ivan Rodriguez Nunez,
    • Jerry Jenkins,
    • Whitley V. Kelley,
    • E. Martina Bebin,
    • Michael A. Lopez,
    • Anna C.E. Hurst,
    • Bruce R. Korf,
    • Jeremy Schmutz,
    • Jane Grimwood,
    • and Gregory M. Cooper
    Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
    ...proband contigs was 29.05 Mb (Table 1).View this table: In this window In a new window Table 1. Demographics, and sequencing and assembly metrics for the cohortHiFi reads were aligned to hg38, and variant calling was performed using DeepVariant (Poplin et al. 2018) and pbsv (https...
  3. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...Model (Edge and Bansal 2019). While statistics-based tools offer faster runtimes, machine learning methods like DeepVariant (Poplin et al. 2018) and Clair (Zheng et al. 2022) are now preferred for both short- and long-read variant calling due to their higher accuracy. However, these machine learning...
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