Searching journal content for articles similar to Chen et al. 24 (2): 310.

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  1. Method: GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
    • Daniel L. Cameron,
    • Jan Schröder,
    • Jocelyn Sietsma Penington,
    • Hongdo Do,
    • Ramyar Molania,
    • Alexander Dobrovic,
    • Terence P. Speed,
    • and Anthony T. Papenfuss
    Genome Res. December 2017 27: 2050-2060; Published in Advance November 2, 2017, doi:10.1101/gr.222109.117
    ...assembly to validate the breakpoint calls (e.g., Manta [Chen et al. 2016], SVMerge [Wong et al. 2010], TIGRA [Chen et al. 2014]). Windowed breakpoint assembly has been used (e.g., SOAPindel [Li et al. 2013], DISCOVAR [Weisenfeld et al. 2014]), but detection is limited to events smaller than the window size...
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  2. Research: Accelerated rates of large-scale mutations in the presence of copper and nickel
    • Frédéric J.J. Chain,
    • Jullien M. Flynn,
    • James K. Bull,
    • and Melania E. Cristescu
    Genome Res. January 2019 29: 64-73; Published in Advance November 28, 2018, doi:10.1101/gr.234724.118
    ...deletion, reads that mapped around putative breakpoint boundaries were assembled using TIGRA-SV v0.4 (Chen et al. 2014). Assembled contigs were then realigned to the reference to define breakpoints using AGE v0.4 (Abyzov and Gerstein 2011). Filtering was performed to assign breakpoints with high confidence...
  3. Method: HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
    • Xian Fan,
    • Mark Chaisson,
    • Luay Nakhleh,
    • and Ken Chen
    Genome Res. May 2017 27: 793-800; Published in Advance January 19, 2017, doi:10.1101/gr.214767.116
    ...of genomic structural variation. Nat Methods 6: 677–681. Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. 2014. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res 24: 310–317. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, MullerWEG,Wetter T, Suhai S. 2004. Using...
  4. Method: SvABA: genome-wide detection of structural variants and indels by local assembly
    • Jeremiah A. Wala,
    • Pratiti Bandopadhayay,
    • Noah F. Greenwald,
    • Ryan O'Rourke,
    • Ted Sharpe,
    • Chip Stewart,
    • Steve Schumacher,
    • Yilong Li,
    • Joachim Weischenfeldt,
    • Xiaotong Yao,
    • Chad Nusbaum,
    • Peter Campbell,
    • Gad Getz,
    • Matthew Meyerson,
    • Cheng-Zhong Zhang,
    • Marcin Imielinski,
    • and Rameen Beroukhim
    Genome Res. April 2018 28: 581-591; Published in Advance March 13, 2018, doi:10.1101/gr.221028.117
    ...(Ye et al. 2009), or from targeted sequence assemblies such as in SOAPindel (Li et al. 2013), Scalpel (Narzisi et al. 2014), ScanIndel (Yang et al. 2015), BreaKmer (Abo et al. 2015), and laSV (Zhuang and Weng 2015). For larger SVs, the cornerstone of most alignment-based detection algorithms...
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