Searching journal content for articles similar to Zerbino and Birney.

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  1. Method: Geometric deep learning framework for de novo genome assembly
    • Lovro Vrček,
    • Xavier Bresson,
    • Thomas Laurent,
    • Martin Schmitz,
    • Kenji Kawaguchi,
    • and Mile Šikić
    Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
    ...are linked by an edge. The next step, layout, is tasked with placing the reads in the correct order—which is equivalent to finding a path through the graph—and is the core of the assembly. An alternative paradigm, based on finding paths in de Bruijn graphs, has been developed shortly after (Idury...
  2. Method: De novo reconstruction of satellite repeat units from sequence data
    • Yujie Zhang,
    • Justin Chu,
    • Haoyu Cheng,
    • and Heng Li
    Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
    ...of the woods fungus, Laetiporus sulphureus (Bull.) Murrill, 1920. Wellcome Open Res 7: 83. doi:10.12688/wellcomeopenres.17750.1 ↵Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821–829. doi:10.1101/gr.074492.107 ↵Zhang L, Hu J, Han X, Li J...
  3. Resource: Assemblathon 1: A competitive assessment of de novo short read assembly methods
    • Dent Earl,
    • Keith Bradnam,
    • John St. John,
    • Aaron Darling,
    • Dawei Lin,
    • Joseph Fass,
    • Hung On Ken Yu,
    • Vince Buffalo,
    • Daniel R. Zerbino,
    • Mark Diekhans,
    • Ngan Nguyen,
    • Pramila Nuwantha Ariyaratne,
    • Wing-Kin Sung,
    • Zemin Ning,
    • Matthias Haimel,
    • Jared T. Simpson,
    • Nuno A. Fonseca,
    • İnanç Birol,
    • T. Roderick Docking,
    • Isaac Y. Ho,
    • Daniel S. Rokhsar,
    • Rayan Chikhi,
    • Dominique Lavenier,
    • Guillaume Chapuis,
    • Delphine Naquin,
    • Nicolas Maillet,
    • Michael C. Schatz,
    • David R. Kelley,
    • Adam M. Phillippy,
    • Sergey Koren,
    • Shiaw-Pyng Yang,
    • Wei Wu,
    • Wen-Chi Chou,
    • Anuj Srivastava,
    • Timothy I. Shaw,
    • J. Graham Ruby,
    • Peter Skewes-Cox,
    • Miguel Betegon,
    • Michelle T. Dimon,
    • Victor Solovyev,
    • Igor Seledtsov,
    • Petr Kosarev,
    • Denis Vorobyev,
    • Ricardo Ramirez-Gonzalez,
    • Richard Leggett,
    • Dan MacLean,
    • Fangfang Xia,
    • Ruibang Luo,
    • Zhenyu Li,
    • Yinlong Xie,
    • Binghang Liu,
    • Sante Gnerre,
    • Iain MacCallum,
    • Dariusz Przybylski,
    • Filipe J. Ribeiro,
    • Shuangye Yin,
    • Ted Sharpe,
    • Giles Hall,
    • Paul J. Kersey,
    • Richard Durbin,
    • Shaun D. Jackman,
    • Jarrod A. Chapman,
    • Xiaoqiu Huang,
    • Joseph L. DeRisi,
    • Mario Caccamo,
    • Yingrui Li,
    • David B. Jaffe,
    • Richard E. Green,
    • David Haussler,
    • Ian Korf,
    • and Benedict Paten
    Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
    ....com/berry.phtml?topic=OligoZip). These word look-up tables were then extended into de Bruijn graphs to allow for global analyses (Pevzner et al. 2001), e.g., Euler (Chaisson and Pevzner 2008), AllPaths (Butler et al. 2008), and Velvet (Zerbino and Birney 2008). As projects grew in scale, further engineering was required to fit large whole...
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  4. Review: Genome graphs and the evolution of genome inference
    • Benedict Paten,
    • Adam M. Novak,
    • Jordan M. Eizenga,
    • and Erik Garrison
    Genome Res. May 2017 27: 665-676; Published in Advance March 30, 2017, doi:10.1101/gr.214155.116
    ...are used to infer a pair of representative linear haploid s for a sample, denoted as paths through the HMM. These sequences are then used for realignment with the succinct self-index-based BWA backtrack, in order to produce a final set of read alignments. More broadly, de Bruijn graph–based tools...
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  5. Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
    • Rei Kajitani,
    • Kouta Toshimoto,
    • Hideki Noguchi,
    • Atsushi Toyoda,
    • Yoshitoshi Ogura,
    • Miki Okuno,
    • Mitsuru Yabana,
    • Masayuki Harada,
    • Eiji Nagayasu,
    • Haruhiko Maruyama,
    • Yuji Kohara,
    • Asao Fujiyama,
    • Tetsuya Hayashi,
    • and Takehiko Itoh
    Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
    ...Assemblathon 2 (Bradnam et al. 2013), are described here. Results Algorithm overview Platanus is divided into three subprograms—Contig-assembly (Fig. 1A), Scaffolding (Fig. 1B), and Gap-close (Fig. 1C)—similar to existing de Bruijn-graph-based assemblers (e.g., SOAPdenovo [Li et al. 2010] and Velvet [Zerbino...
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  6. Resource: De novo assembly of human genomes with massively parallel short read sequencing
    • Ruiqiang Li,
    • Hongmei Zhu,
    • Jue Ruan,
    • Wubin Qian,
    • Xiaodong Fang,
    • Zhongbin Shi,
    • Yingrui Li,
    • Shengting Li,
    • Gao Shan,
    • Karsten Kristiansen,
    • Songgang Li,
    • Huanming Yang,
    • Jian Wang,
    • and Jun Wang
    Genome Res. February 2010 20: 265-272; Published in Advance December 17, 2009, doi:10.1101/gr.097261.109
    ...of short DNA sequences using SSAKE. Bioinformatics 23: 500–501. Zerbino DR, Birney E. 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821–829. Received June 14, 2009; accepted in revised form October 19, 2009. Li et al. 272 Genome Research www..org De novo...
  7. Method: TransRate: reference-free quality assessment of de novo transcriptome assemblies
    • Richard Smith-Unna,
    • Chris Boursnell,
    • Rob Patro,
    • Julian M. Hibberd,
    • and Steven Kelly
    Genome Res. August 2016 26: 1134-1144; Published in Advance June 1, 2016, doi:10.1101/gr.196469.115
    ...scores revealed that on different data sets, different assemblers tended to producemore accurate assemblies (Fig. 5B). On average, Oases (version 0.2.06with Velvet version 1.2.07) produced the highestmean contig scores for mouse and rice, whereas Trinity (version TrinityFigure 4. TransRate contig score...
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  8. Resource: ECHO: A reference-free short-read error correction algorithm
    • Wei-Chun Kao,
    • Andrew H. Chan,
    • and Yun S. Song
    Genome Res. July 2011 21: 1181-1192; Published in Advance April 11, 2011, doi:10.1101/gr.111351.110
    ...ECHO: A reference-free short-read error correction algorithm Wei-Chun Kao 1 , Andrew H. Chan 1 and Yun S. Song 1 , 2 , 3 1Computer Science Division, University of California, Berkeley, California 94721, USA; 2Department...
  9. Method: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
    • Sergey Koren,
    • Brian P. Walenz,
    • Konstantin Berlin,
    • Jason R. Miller,
    • Nicholas H. Bergman,
    • and Adam M. Phillippy
    Genome Res. May 2017 27: 722-736; Published in Advance March 15, 2017, doi:10.1101/gr.215087.116
    ...and outperforms hybrid methods with as little as 20× single-molecule coverage. At higher coverage, reference-quality de novo assemblies are possible, including the complete assembly of euchromatic chromosomes from either PacBio or Nanopore sequencing. In addition, Canu’s improved graph construction algorithm...
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  10. Resource: Dindel: Accurate indel calls from short-read data
    • Cornelis A. Albers,
    • Gerton Lunter,
    • Daniel G. MacArthur,
    • Gilean McVean,
    • Willem H. Ouwehand,
    • and Richard Durbin
    Genome Res. June 2011 21: 961-973; Published in Advance October 27, 2010, doi:10.1101/gr.112326.110
    ...such variations. The first paradigm is to perform de novo assembly of short reads and detect indels by comparing contigs to a reference sequence. The second paradigm is to map each fragment directly and independently of other fragments to the reference sequence using a read mapper (e.g., Li et al. 2008; Langmead...
    OPEN ACCESS ARTICLE
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