Searching journal content for articles similar to Cameron et al. 27 (12): 2050.

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  1. Method: Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
    • Andrea Cracco and
    • Alexandru I. Tomescu
    Genome Res. July 2023 33: 1198-1207; Published in Advance May 30, 2023, doi:10.1101/gr.277615.122
    ...Bruijn graphs are one of the most fundamental data structures in computational genomics. Colored compacted de Bruijn graphs are a variant built on a collection of sequences and associate to each k-mer the sequences in which it appears. We present GGCAT, a tool for constructing both types of graphs, based...
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  2. Method: Detection of simple and complex de novo mutations with multiple reference sequences
    • Kiran V. Garimella,
    • Zamin Iqbal,
    • Michael A. Krause,
    • Susana Campino,
    • Mihir Kekre,
    • Eleanor Drury,
    • Dominic Kwiatkowski,
    • Juliana M. Sá,
    • Thomas E. Wellems,
    • and Gil McVean
    Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
    ...was unaffected by relaxing the restriction that events be identified on the correct haplotypic background.The other SV detection methods (GRIDSS and Manta), and SNV/small indel caller (HaplotypeCaller) underperformed considerably at DNM detection compared with Corticall and DELLY. Although poor sensitivity...
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  3. Method: Long-read reconstruction of many diverse haplotypes with devider
    • Jim Shaw,
    • Christina Boucher,
    • Yun William Yu,
    • Noelle Noyes,
    • and Heng Li
    Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
    ...techniques. Here, we present devider, an algorithm for haplotyping small sequences, such as viruses or genes, from long-read sequencing. devider uses a positional de Bruijn graph with sequence-to-graph alignment on an alphabet of informative alleles to provide a fast assembly-inspired approach compatible...
  4. Method: Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer
    • Eva K.F. Chan,
    • Daniel L. Cameron,
    • Desiree C. Petersen,
    • Ruth J. Lyons,
    • Benedetta F. Baldi,
    • Anthony T. Papenfuss,
    • David M. Thomas,
    • and Vanessa M. Hayes
    Genome Res. May 2018 28: 726-738; Published in Advance April 4, 2018, doi:10.1101/gr.227975.117
    ...Acids Res 45: e162. ↵Cameron DL, Schröder J, Penington JS, Do H, Molania R, Dobrovic A, Speed TP, Papenfuss AT. 2017. GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Res 27: 2050–2060. ↵Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S...
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  5. Research: The motif composition of variable number tandem repeats impacts gene expression
    • Tsung-Yu Lu,
    • Paulina N. Smaruj,
    • Geoffrey Fudenberg,
    • Nicholas Mancuso,
    • and Mark J.P. Chaisson
    Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
    ...al. 2020). However, variant calling remains challenging for multiallelic VNTR regions as the position of calls varies (Li et al. 2020); an extra processing step is needed to reveal the multiallelic property of a locus.Another commonly used graph model is the de Bruijn graph (dBG). The main...
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