Searching journal content for articles similar to Lorig-Roach et al. 34 (3): 454.

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  1. 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
    ...-C chromosome conformation capture data for both phasing and scaffolding of the assembly graph and supports both short-read Hi-C as well as Nanopore-based Pore-C (Deshpande et al. 2022) sequencing data. Critically, Verkko integrates this long-range linkage information directly with the assembly graph, improving...
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  2. Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
    • Sergey Koren,
    • Zhigui Bao,
    • Andrea Guarracino,
    • Shujun Ou,
    • Sara Goodwin,
    • Katharine M. Jenike,
    • Julian Lucas,
    • Brandy McNulty,
    • Jimin Park,
    • Mikko Rautiainen,
    • Arang Rhie,
    • Dick Roelofs,
    • Harrie Schneiders,
    • Ilse Vrijenhoek,
    • Koen Nijbroek,
    • Olle Nordesjo,
    • Sergey Nurk,
    • Mike Vella,
    • Katherine R. Lawrence,
    • Doreen Ware,
    • Michael C. Schatz,
    • Erik Garrison,
    • Sanwen Huang,
    • William Richard McCombie,
    • Karen H. Miga,
    • Alexander H.J. Wittenberg,
    • and Adam M. Phillippy
    Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
    ...additionally processed the 50× assembly with Hi-C and Pore-C data using GFAse (Lorig-Roach et al. 2024) integration within Verkko (Table 1; Supplemental Table 2). The assemblies generated using either trio, Hi-C, or Pore-C information for phasing haplotypes had similar scaffold, QV, gene completeness, and T2T...
  3. Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
    • William T. Harvey,
    • Peter Ebert,
    • Jana Ebler,
    • Peter A. Audano,
    • Katherine M. Munson,
    • Kendra Hoekzema,
    • David Porubsky,
    • Christine R. Beck,
    • Tobias Marschall,
    • Kiran Garimella,
    • and Evan E. Eichler
    Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
    ...and phasing. Methods such as Shasta (Shafin et al. 2020), wtdbg2 (Ruan and Li 2020), and Canu (Koren et al. 2017) show considerable promise, yet currently contiguous, haplotype-phased assemblies are not as easily generated and thus have not been used as frequently in recent studies.SNV calling with assembly...
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