Searching journal content for articles similar to Kamath et al. 27 (5): 747.

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  1. Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
    • Matthias H. Weissensteiner,
    • Andy W.C. Pang,
    • Ignas Bunikis,
    • Ida Höijer,
    • Olga Vinnere-Petterson,
    • Alexander Suh,
    • and Jochen B.W. Wolf
    Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
    ...assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM...
  2. Resource: Recompleting the Caenorhabditis elegans genome
    • Jun Yoshimura,
    • Kazuki Ichikawa,
    • Massa J. Shoura,
    • Karen L. Artiles,
    • Idan Gabdank,
    • Lamia Wahba,
    • Cheryl L. Smith,
    • Mark L. Edgley,
    • Ann E. Rougvie,
    • Andrew Z. Fire,
    • Shinichi Morishita,
    • and Erich M. Schwarz
    Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
    ..., classical mutagenesis, and engineering.Genome assembly and local reassemblyWe assembled raw PacBio reads with the long-read assemblers Canu (Koren et al. 2017), FALCON (Chin et al. 2016), miniasm (Li 2016), and HINGE (Kamath et al. 2017); each used different algorithms to handle repeats and hence could...
    OPEN ACCESS ARTICLE
  3. Resource: Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
    • Wenjuan Yu,
    • Haohui Luo,
    • Jinbao Yang,
    • Shengchen Zhang,
    • Heling Jiang,
    • Xianjia Zhao,
    • Xingqi Hui,
    • Da Sun,
    • Liang Li,
    • Xiu-qing Wei,
    • Stefano Lonardi,
    • and Weihua Pan
    Genome Res. February 2024 34: 326-340; Published in Advance March 1, 2024, doi:10.1101/gr.278232.123
    ...) are based on the de Bruijn graph. ABruijn combines de Bruijin and the overlap-layout-consensus approaches. Flye uses the repeat graph, which extends the de Bruijn graph so that it can deal with the errors in long reads. wtdbg2 also uses a combination of overlap graph and de Bruijin graph (Ruan and Li 2020...
  4. Editorial: New advances in sequence assembly
    • Adam M. Phillippy
    Genome Res. May 2017 27: xi-xiii; doi:10.1101/gr.223057.117
    ..., Xia F , Courtade TA , Tse DN . 2017 . HINGE: long-read assembly achieves optimal repeat resolution . Genome Res ( this issue ). doi: 10.1101/gr.216465.116 . ↵ Kaplan N , Dekker J . 2013 . High-throughput scaffolding from in vivo DNA interaction frequency . Nat Biotechnol 31 : 1143 – 1147 . ↵ Khost DE...
    OPEN ACCESS ARTICLE
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