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Development of denovo genome/gene assembler for highly heterozygous samples from NGS sequence data

Research Project

Project/Area Number 24310142
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Genome biology
Research InstitutionTokyo Institute of Technology

Principal Investigator

ITOH TAKEHIKO  東京工業大学, 生命理工学研究科, 教授 (90501106)

Co-Investigator(Kenkyū-buntansha) NOGUCHI Hideki  国立遺伝学研究所, 先端ゲノミクス推進センター, 特任准教授 (50333349)
MARUYAMA Haruhiko  宮崎大学, 医学部, 教授 (90229625)
Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥20,930,000 (Direct Cost: ¥16,100,000、Indirect Cost: ¥4,830,000)
Fiscal Year 2014: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Fiscal Year 2013: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2012: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Keywordsゲノム情報 / バイオインフォマティクス / ゲノム情報解析 / アセンブラ / 遺伝子予測
Outline of Final Research Achievements

Assembling the highly heterozygous diploid genomes is a big scientific challenge due to the increased complexity of the de Bruijn graph structure. To deal with an increasing demand for sequencing of non-model and/or wild-type sample, we developed a novel de novo assembler, Platanus, which can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments into contigs by constructing de Bruijn graphs, followed by scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step.
We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, the Platanus assembly results have a larger NG50 length without any accompanying loss of accuracy in both simulated data and real data including highly heterozygous Strongyloides samples.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (5 results)

All 2014 2013 2012

All Journal Article (1 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (4 results)

  • [Journal Article] Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.2014

    • Author(s)
      R. Kajitani, K. Toshimoto, H. Noguchi, A. Toyoda, Y. Ogura, M. Okuno, M. Yabana, M. Harada, E. Nagayasu, H. Maruyama, Y. Kohara, A. Fujiyama, T. Hayashi and T.Itoh
    • Journal Title

      Genome Research,

      Volume: 24 Issue: 8 Pages: 1384-1384

    • DOI

      10.1101/gr.170720.113

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] メタゲノム用de novoアセンブラの開発およびilluminaデータを用いたベンチマーク2014

    • Author(s)
      梶谷嶺
    • Organizer
      ゲノム微生物学会
    • Place of Presentation
      東京農工大学
    • Related Report
      2013 Annual Research Report
  • [Presentation] イトマキヒトデのde novoアセンブリ2013

    • Author(s)
      西村智洋
    • Organizer
      日本動物学会
    • Place of Presentation
      岡山大学
    • Related Report
      2013 Annual Research Report
  • [Presentation] 高ヘテロ接合性を持つベネズエラ糞線虫のゲノム解析2012

    • Author(s)
      矢花充, 他
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2012-12-11
    • Related Report
      2012 Annual Research Report
  • [Presentation] 高ヘテロ接合性ゲノムのde novoアセンブリ2012

    • Author(s)
      梶谷嶺, 他
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2012-12-11
    • Related Report
      2012 Annual Research Report

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Published: 2012-04-24   Modified: 2019-07-29  

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