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The Development of a cloud computing-based annotation system for next-generation sequencing data

Research Project

Project/Area Number 24510273
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Genome biology
Research InstitutionNational Institute of Genetics

Principal Investigator

NAGASAKI Hideki  国立遺伝学研究所, 生命情報研究センター, 特任研究員 (70624451)

Co-Investigator(Renkei-kenkyūsha) KAMINUMA Eli  国立遺伝学研究所, 生命情報研究センター, 助教 (90314559)
Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2014: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2013: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2012: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywordsゲノム / 次世代シーケンサー / 解析パイプライン / クラウド / RNA-Seq / ChIP-Seq / HLA / リシーケンス / SNP / de novoアセンブリ / クラウドコンピューティング / denovo アセンブル
Outline of Final Research Achievements

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge.

Report

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

    (26 results)

All 2015 2014 2013 2012 Other

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 1 results) Presentation (17 results) (of which Invited: 5 results) Book (2 results) Remarks (5 results)

  • [Journal Article] A Bead-based Normalization for Uniform Sequencing depth (BeNUS) protocol for multi-samples sequencing exemplified by HLA-B2014

    • Author(s)
      Hosomichi K, Mitsunaga S, Nagasaki H, Inoue Ituro.
    • Journal Title

      BMC Genomics

      Volume: 15 Issue: 1 Pages: 645-645

    • DOI

      10.1186/1471-2164-15-645

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data.2013

    • Author(s)
      Nagasaki H, Mochizuki T, Kodama Y, Saruhashi S, Morizaki S, Sugawara H, Ohyanagi H, Kurata N, Okubo K, Takagi T, Kaminuma E, Nakamura Y.
    • Journal Title

      DNA Res.

      Volume: 20 Pages: 383-390

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] HLA解析ツール2015

    • Author(s)
      長崎英樹
    • Organizer
      GalaxyWorkshopTokyo2015
    • Place of Presentation
      東京大学 先端科学技術研究センター
    • Year and Date
      2015-04-28
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] The Construction of Genome Annotation Database for Liverwort Marchantia polymorpha2015

    • Author(s)
      長崎英樹、石崎公庸、大和勝幸、河内孝之、中村保一
    • Organizer
      第56回日本植物生理学会年会
    • Place of Presentation
      東京農業大学
    • Year and Date
      2015-03-16 – 2015-03-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] DDBJ Read Annotation Pipeline の紹介と実習 (RNA-Seq配列のde novoアセンブリを中心に)2015

    • Author(s)
      長崎英樹
    • Organizer
      ゲノム支援講習会
    • Place of Presentation
      国立遺伝学研究所
    • Year and Date
      2015-02-28
    • Related Report
      2014 Annual Research Report
  • [Presentation] The Construction of Genome Annotation Database for Liverwort Marchantia polymorpha2015

    • Author(s)
      Hideki Nagasaki Kimitsune Ishizaki Katsuyuki T. Yamato Takayuki Kohchi Yasukazu Nakamura
    • Organizer
      International Plant & Animal Genome XXIII
    • Place of Presentation
      San Diego, CA, USA
    • Year and Date
      2015-01-10 – 2015-01-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] DDBJ Read Annotation Pipeline の紹介と実習2014

    • Author(s)
      長崎英樹
    • Organizer
      第30回 DDBJing 講習会 in 東京
    • Place of Presentation
      独立行政法人 科学技術振興機構 東京本部
    • Year and Date
      2014-12-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] The Construction of Genome Annotation Database for the Liverwort Marchantia polymorpha2014

    • Author(s)
      Hideki Nagasaki Naoko Iida Yasukazu Nakamura
    • Organizer
      Marchantia Workshop 2014
    • Place of Presentation
      神戸大学
    • Year and Date
      2014-12-08 – 2014-12-10
    • Related Report
      2014 Annual Research Report
  • [Presentation] The Construction of Genome Annotation Database for Liverwort ゼニゴケゲノムアノテーションデータベースの構築2014

    • Author(s)
      長崎英樹、石崎公庸、大和勝幸、河内孝之、中村保一
    • Organizer
      第37回 日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] DDBJ Read Annotation Pipeline の紹介と実習(RNA-Seq配列のde novoアセンブリを中心に)2014

    • Author(s)
      長崎英樹
    • Organizer
      AJACS十勝
    • Place of Presentation
      帯広畜産大学
    • Year and Date
      2014-09-12
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Liverwort Genome Analysis Using DDBJ Pipeline and Construction of the Database Annotated by the Research Communities2014

    • Author(s)
      Nagasaki H, Ishizaki K, Yamato K T, Kohchi T, Nakamura Y.
    • Organizer
      International Plant & Animal Genome XXII
    • Place of Presentation
      サンディエゴ、米国
    • Related Report
      2013 Research-status Report
  • [Presentation] Liverwort Genome Analysis and Construction of the Genome Annotation Database: ゼニゴケゲノム解析とゲノムアノテーションデータベースの構築2014

    • Author(s)
      Nagasaki H, Ishizaki K, Yamato K T, Kohchi T, Nakamura Y.
    • Organizer
      第55回 日本植物生理学会年会
    • Place of Presentation
      富山大学
    • Related Report
      2013 Research-status Report
  • [Presentation] Liverwort Genome Analysis and Construction of the Genome Annotation Database: ゼニゴケゲノム解析とゲノムアノテーションデータベースの構築2013

    • Author(s)
      Nagasaki H, Ishizaki K, Yamato K T, Kohchi T, Nakamura Y.
    • Organizer
      JSBi2013
    • Place of Presentation
      タワーホール船堀
    • Related Report
      2013 Research-status Report
  • [Presentation] Liverwort Genome Analysis and Construction of the Genome Annotation Database: ゼニゴケゲノム解析とゲノムアノテーションデータベースの構築2013

    • Author(s)
      Nagasaki H, Ishizaki K, Yamato K T, Kohchi T, Nakamura Y.
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Related Report
      2013 Research-status Report
  • [Presentation] Our Informatics Approaches for Marchantia Genome2013

    • Author(s)
      Nagasaki H, Iida N, Nakamura Y.
    • Organizer
      Marchantia IV
    • Place of Presentation
      メルボルン、オーストラリア
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Liverwort Genome Analysis using DDBJ Pipeline and Construction of the Genome Annotation Database2013

    • Author(s)
      Hideki Nagasaki, Takatomo Fujisawa, Takako Mochizuki, Eli Kaminuma, Yasukazu Nakamura et al.
    • Organizer
      International Plant & Animal Genome XXI
    • Place of Presentation
      San Diego, CA, USA
    • Related Report
      2012 Research-status Report
  • [Presentation] DDBJパイプラインによるゼニゴケゲノム解析とゲノムアノテーションデータベースの構築2012

    • Author(s)
      長崎 英樹, 藤澤 貴智, 望月 孝子, 神沼 英里, 中村 保一ら
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡
    • Related Report
      2012 Research-status Report
  • [Presentation] DDBJパイプラインによる高速シーケンスデータ解析2012

    • Author(s)
      長崎 英樹, 望月 孝子
    • Organizer
      統合データベース講習会 : AJACS名古屋
    • Place of Presentation
      名古屋大学 工学部ES館 サテライトラボラトリーES031
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] NIGスパコンを利用したNGSアーカイブ配列再利用とクラウド型解析パイプライン実習2012

    • Author(s)
      長崎 英樹, 望月 孝子
    • Organizer
      第164回農林交流センターワークショップ
    • Place of Presentation
      農林水産省農林水産技術会議事務局筑波事務所 情報通信共同利用館(電農館)3階セミナー室
    • Related Report
      2012 Research-status Report
    • Invited
  • [Book] 実験医学別冊 「次世代シークエンス解析スタンダード」2014

    • Author(s)
      長崎英樹、望月孝子、谷沢靖洋、神沼英里、中村保一
    • Total Pages
      8
    • Publisher
      羊土社
    • Related Report
      2014 Annual Research Report
  • [Book] 実験医学増刊Vol.32 No.20 「今日から使える! データベース・ウェブツール 達人になるための実践ガイド100」2014

    • Author(s)
      長崎英樹
    • Total Pages
      4
    • Publisher
      羊土社
    • Related Report
      2014 Annual Research Report
  • [Remarks] DDBJ Read Annotation Pipeline

    • URL

      http://p.ddbj.nig.ac.jp

    • Related Report
      2014 Annual Research Report
  • [Remarks] DDBJ Read Annotation Pipeline 基礎解析部

    • URL

      http://p.ddbj.nig.ac.jp/

    • Related Report
      2013 Research-status Report
  • [Remarks] DDBJ Read Annotation Pipeline 高次解析部

    • URL

      http://p-galaxy.ddbj.nig.ac.jp

    • Related Report
      2013 Research-status Report
  • [Remarks] DDBJ Read Annotation Pipeline Basic Analysis

    • URL

      http://p.ddbj.nig.ac.jp/

    • Related Report
      2012 Research-status Report
  • [Remarks] DDBJ Read Annotation Pipeline High-Level Analysis

    • URL

      http://p-galaxy.ddbj.nig.ac.jp/

    • Related Report
      2012 Research-status Report

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Published: 2013-05-31   Modified: 2019-07-29  

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