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Tools and Webapps for Public High-Throughput Sequencing Database

Tools and Webapps for Public High-Throughput Sequencing Database

An introduction of our activity for public database for high-throughput sequencing, presented at #Illumina #BaseSpace Worldwide Developers Conference 2014 in Japan at #DBCLS

Tazro Inutano Ohta

October 29, 2014
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  1. %#$-4ʹ͓͚Δ/(4ʹର͢ΔऔΓ૊Έʹ͍ͭͯ Research Institute for Information and Systems Database Center for

    Life Science Tazro Ohta <[email protected]> ! prepared for Illumina's BaseSpace Worldwide Developers Conference in Japan October 28, 2014 5PPMTBOE8FCBQQTGPS1VCMJD)JHI5ISPVHIQVU4FRVFODJOH%BUBCBTF
  2. Web Tools by DBCLS, for Deep Sequencing Raw Data Repository

    Search Sequence Search Tools Galaxy Pipeline Agenda For Developers: Programmable Options DBCLS SRA API G2-series API TogoWS
  3. Web Tools by DBCLS, for Deep Sequencing Raw Data Repository

    Search DBCLS SRA <sra.dbcls.jp> DBCLS AOE <aoe.dbcls.jp> Sequence Search Tools GGRNA <ggrna.dbcls.jp> GGGenome <gggenome.dbcls.jp> Galaxy Pipeline DBCLS Galaxy <galaxy.dbcls.jp> Pitagora-Galaxy <pitagora-galaxy.org> Agenda
  4. Raw Data Repository Search DBCLS SRA Statistics of Sequence Read

    Archive Extended Metadata Full-text Search Engine DBCLS AOE Statistics of ArrayExpress by EBI Interactive Visualization Faceted Search
  5. Sequence Search Tools GGRNA Ultrafast Text Search for genes and

    transcripts Against all organisms in RefSeq Best for short nucleotide sequence search GGGenome Ultrafast Text Search for Ref. Genome Mismatches/gaps CRISPR/Cas Design Feature <coming soon!>
  6. Galaxy Pipeline DBCLS Galaxy Public galaxy server + VMWare OpenID

    login Original Tutorial Videos Pitagora-Galaxy Portable pre-configured Galaxy VirtualMachine/Docker Container Monthly Galaxy Workshop in Tokyo
  7. For Developers: Programmable Options DBCLS SRA Data Retrieve Search API

    Quality API <coming soon> G2-series API TogoWS
  8. Web Tools by DBCLS, for Deep Sequencing Raw Data Repository

    Search Sequence Search Tools Galaxy Pipeline For Developers: Programmable Options DBCLS SRA API G2-series API TogoWS