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Development of NGS Data Analysis Softwares Considering the Data Profile of Each Platform

Research Project

Project/Area Number 26430199
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field System genome science
Research InstitutionMaebashi Institute of Technology

Principal Investigator

Nakamura Kensuke  前橋工科大学, 工学部, 教授 (20212095)

Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2014: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords次世代シーケンサー / イルミナ / Gef-seq / 相同組換変異解析 / 転写因子 / 解析プログラム開発 / エラープロファイル / ゲノムアセンブル / マッピング / バイオインフォマティクス / 相同組換え / 変異解析 / 機器特異的エラープロファイル / Illumina / 相同組み替え / 酵母 / プログラム開発 / 微生物ゲノム / ChIP-seq
Outline of Final Research Achievements

I have been developing a mapping program "maps" suite for next generation sequencing. I was able to achieve the following accomplishment during the 3 years period. (1) I have contributed the establishment of Gef-seq (Genome footprint sequence) analysis method, which is an improved method of ChIP-seq analysis, by preparing the computational analysis pipeline. (2) I continued the error-profile analysis of Illumina Next generation sequencer. (3) I have contributed the analysis of homologous/non-homologous rearrangements occuring in a part of organera genomes. (4) I contributed a comparative genome analysis of several yeast strains by genome assembling. For (1), we published a apaper and made our program public, and preparing another manuscript to describe the protocol. For (2), I made a couple of presentations. For (3) and (4), we are preparing for a publication.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (5 results)

All 2017 2016 2015 2014

All Journal Article (1 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 1 results,  Acknowledgement Compliant: 1 results) Presentation (3 results) Book (1 results)

  • [Journal Article] Genome-wide Identification of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by in vivo Footprinting2017

    • Author(s)
      Onuma Chumsakul, Divya P. Anantsuri, Tak Quirke, Taku Oshima, Kensuke Nakamura, Shu Ishikawa and Michiko M. Nakano
    • Journal Title

      Journal of Bacteriology

      Volume: 199

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] プラットフォームの特性を考慮した次世代シーケンサーデータ解析技術基盤の整備2016

    • Author(s)
      竹内敬一郎・中村建介
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2016-12-01
    • Related Report
      2016 Annual Research Report
  • [Presentation] 次世代シーケンサーのベースコール精度の検証2015

    • Author(s)
      松本秀太・中村建介
    • Organizer
      第38回分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2015-12-01
    • Related Report
      2015 Research-status Report
  • [Presentation] Gef-seqに対応したマッピングプログラムおよびGUIの開発2015

    • Author(s)
      中村建介・松本秀太
    • Organizer
      第9回日本ゲノム微生物学会年会
    • Place of Presentation
      神戸大学
    • Year and Date
      2015-03-06 – 2015-03-08
    • Related Report
      2014 Research-status Report
  • [Book] 「高精度で結合領域を決定する」次世代シーケンス解析スタンダード・NGSのポテンシャルを活かしきるWET&DRY2014

    • Author(s)
      大島拓・石川周・Onuma Chumsakul・中村建介 / 二階堂愛 編
    • Publisher
      羊土社
    • Related Report
      2014 Research-status Report

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Published: 2014-04-04   Modified: 2018-03-22  

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