Searching journal content for articles similar to Cooke et al..

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  1. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...), and the X and Y Chromosomes (Wagner et al. 2025). The latest draft benchmarks currently being evaluated by GIAB are based on a T2T assembly of HG002 and include 3.6 million SNVs, 950,000 indels, and 29,000 SVs in 2.74 and 2.76 Gbp of GRCh38 (2.77 and 2.82 Gbp of CHM13) for small variants and SVs...
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  2. Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
    • Zepu Miao and
    • Jia-Xing Yue
    Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
    ...) while being less discriminative for small variants such as single-nucleotide variants (SNVs) and small insertion/deletions (indels) during graph construction; therefore, a pan graph constructed by Minigraph is not a strictly lossless representation of the full genomic variation carried by input s...
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  3. 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
    ...enabled us to assess concordance with the Genome in a Bottle (GIAB) v4.2.1 benchmark call set (Methods) (Wagner et al. 2022a). This gives an alignment-based measure of polishing accuracy that spans ∼80% of the HG005 , as defined by the GIAB high-confidence regions.With DeepPolisher, we reduce the number...
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