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

• Project/Area Number: 24310142
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Genome biology
• Research Institution: Tokyo 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: ¥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.

Research Products

• [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
  • 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
• [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
• [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
• [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