Development of haplotype phased genome assembler

2018 Fiscal Year Final Research Report

• Project/Area Number: 16H04719
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Genome biology
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: Itoh Takehiko 東京工業大学, 生命理工学院, 教授 (90501106)
• Co-Investigator(Kenkyū-buntansha): 豊田 敦 国立遺伝学研究所, ゲノム・進化研究系, 特任教授 (10267495) ; 梶谷 嶺 東京工業大学, 生命理工学院, 助教 (40756706)
• Project Period (FY): 2016-04-01 – 2019-03-31
• Keywords: ゲノムアセンブラ / ヘテロ接合性

Outline of Final Research Achievements

The ultimate goal for diploid genome determination is to completely decode homologous chromosomes independently, and several phasing programs from consensus sequences have been developed. These methods work well for lowly heterozygous genomes, but the manifold species have high heterozygosity. Additionally, there are highly divergent regions, where the haplotype sequences differ considerably and are likely to relate to various interesting biological phenomena. However, they cannot be accessed by existing phasing methods, and we have to adopt costly traditional methods. Here, we develop a de novo haplotype assembler, Platanus-allee, which initially constructs each haplotype sequence and then untangles the assembly graphs utilizing sequence links and synteny information. A comprehensive benchmark analysis reveals that Platanus-allee exhibits high recall and precision, particularly for highly divergent regions.

Free Research Field

ゲノム情報

Academic Significance and Societal Importance of the Research Achievements

本研究を通じて開発されたPlatanua-alleeアセンブラは、そのアルゴリズムを論文にて公開する一方で、ホームページより利用可能な形のプログラムとして公開している。このプログラムを用いることで、従来はfosmid構築など特別なコストのかかる方法で配列決定をしないとアクセスできなかったようなゲノム領域に対し、安価なIlluminaデータの使用のみで迫ることができるようになったという点で、学術的な意義は極めて大きいと考えられる。