Public data repository and analysis pipeline for high-throughput sequencing

Transcript

1. ࣍ੈ୅γʔέϯαʔΛར༻ͨ͠ݚڀࣄྫͱͦΕΛࢧ͑Δެڞπʔϧɾσʔλϕʔε Public data repository and analysis pipeline for high-throughput sequencing

   ৘ใɾγεςϜݚڀػߏ ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔ େా ୡ࿠ <t.ohta@dbcls.rois.ac.jp> ! prepared for ୈ186ճ ߬฼ࡉ๔ݚڀձ ྫձ July 11, 2014

2. Agenda ‣ %#$-4ͱ౷߹%#ϓϩδΣΫτʹ͍ͭͯ
   ‣ /(4ʹؔ࿈͢Δσʔλϕʔε
   ‣ /(4Λ࢖ͬͨݚڀϑϩʔʹ͓͚Δެ։%#ͷ໾ׂ
   ‣ ެڞσʔλͷݕࡧ͔Βղੳ·Ͱ

3. DBCLSͱ౷߹σʔλϕʔεϓϩδΣΫτʹ͍ͭͯ Database Integration Project and DBCLS

4. DBCLSͱ౷߹σʔλϕʔεϓϩδΣΫτʹ͍ͭͯ ‣ େֶڞಉར༻ػؔ๏ਓ
   ৘ใɾγεςϜݚڀػߏ 30*4 ࡿԼ
   ‣ +45ࡿԼͷ/#%$
   ಉ͘͡30*4ࡿԼͷҨ఻ݚ%%#+ͱ࿈ܞ
   ‣ /#%$͸ϑΝϯσΟϯάɼ%%#+͸σʔλΞʔΧΠϒɼ%#$-4͸ٕज़։ൃΛ୲౰

   ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔ %#$-4 ͸ɺੜ໋Պֶ෼໺ʹ͓͚Δ
   σʔλެ։ͷଅਐͱσʔλϕʔεߏஙʹࢿ͢Δٕज़ͷݚڀ։ൃΛߦ͏ݚڀॴͰ͢ɻ

5. http://dbcls.rois.ac.jp/about

6. DBCLSͱ౷߹ϓϩδΣΫτ: ͜Ε·Ͱʹ։ൃɾӡ༻͖ͯͨ͠αʔϏε ‣ *OUFHCJP
   σʔλϕʔεΧλϩά
   ‣ ੜ໋ՊֶσʔλϕʔεΞʔΧΠϒ
   ‣ ͦͷଞɼσʔλϕʔεԣஅݕࡧͳͲ%#౷߹ʹࢿ͢ΔαʔϏε
   ‣ ݸผʹݚڀ։ൃΛߦ͍ͬͯΔٕज़ͷԠ༻ͱͯ͠ͷαʔϏε
   

   ‣ UPHPHFOPNF
   ((3/"
   3FG&Y
   ৽ண࿦จϨϏϡʔ
   ౷߹57
   *O.F9FT
   FUD

7. Database of Databases: Integbio DBcatalog http://integbio.jp/dbcatalog

8. ੜ෺छ΍ΧςΰϦʹΑΔߜࠐ͕Մೳ http://integbio.jp/dbcatalog

9. DBͷҡ࣋ɼҾ͖ड͚·͢ http://dbarchive.biosciencedbc.jp/

10. ҰׅDL΍ར༻ڐ୚؅ཧΛαϙʔτ http://dbarchive.biosciencedbc.jp/

11. Find more at http://biosciencedbc.jp

12. togogenome.org ggrna.dbcls.jp refex.dbcls.jp first.lifesciencedb.jp togotv.dbcls.jp docman.dbcls.jp/im

13. togogenome.org ggrna.dbcls.jp refex.dbcls.jp first.lifesciencedb.jp togotv.dbcls.jp docman.dbcls.jp/im ήϊϜ৘ใ/ՄࢹԽ ߴ଎Ԙج഑ྻݕࡧ Ҩ఻ࢠൃݱϦϑΝϨϯε ೔ຊޠ࿦จϨϏϡʔ

    ಈըνϡʔτϦΞϧ ࿦จࣥචαϙʔτ

14. Find more at http://dbcls.rois.ac.jp/services

15. NGSʹؔ࿈͢Δσʔλϕʔε Data Repositories and Databases for high-throughput sequencing

16. NGSʹؔ࿈͢Δσʔλϕʔεɾެ։σʔλϨϙδτϦ ‣ ࠃࡍԘج഑ྻσʔλϕʔεͱ4FRVFODF
    3FBE
    "SDIJWF
    ‣ ڊେϓϩδΣΫτʹΑΔσʔλϗεςΟϯά

17. ࠃࡍԘج഑ྻσʔλϕʔεͱSequence Read Archive ‣ */4%$
    *OU`M
    /VDMFPUJEF
    4FRVFODF
    %BUBCBTF
    $PMMBCPSBUJPO
    ‣ /$#*
    &#*
    %%#+
    ہͷ୲౰νʔϜ͕ڞಉͰӡ༻
    ‣

    4FRVFODF
    3FBE
    "SDIJWF
    /(4ͷͨΊͷ1SJNBSZ
    EBUB
    SFQP www.insdc.org

18. ڊେϓϩδΣΫτʹΑΔσʔλϗεςΟϯά ‣ ن໛ͷେ͖ͳϓϩδΣΫτͰ͸ࣗΒσʔλΛެ։͢Δ৔߹͕͋Δ
    ‣ 
    (FOPNFT
    1SPKFDU
    IUUQHFOPNFTPSH
    ‣ 5IF
    $BODFS
    (FOPNF
    "UMBT
    1SPKFDU
    IUUQUDHBEBUBODJOJIHPW
    ‣ &/$0%&
    1SPKFDU
    IUUQHFOPNFVDTDFEVFODPEF
    ‣

    σʔλͷίϐʔ͕Ϋϥ΢υαʔϏε্ʹެ։͞Ε͍ͯΔ͜ͱ΋
    ‣ HFOPNFT
    PO
    "84
    
    IUUQBXTBNB[PODPNHFOPNFT

19. σʔλͱσʔλϕʔεͷ֊૚ʹ͍ͭͯ Knowledge Summarised Data Experimental Data Knowledge-base Database Primary Data

    Repository Biological Information “Database”

20. NGSʹؔ࿈͢Δσʔλϕʔε Knowledge-base Database Primary Data Repository

21. NGSʹؔ࿈͢Δσʔλϕʔε Knowledge-base Database Primary Data Repository

22. NGSΛ࢖ͬͨݚڀϑϩʔʹ͓͚Δެ։DBͷ໾ׂ The role of database for each steps of sequencing

    research procedure

23. ҰൠతͳNGSΛ༻͍ͨݚڀϑϩʔ ࣮ݧσβΠϯ ༧උ࣮ݧ αϯϓϦϯά DNAௐ੔ ϥΠϒϥϦ࡞੡ γʔέϯε QC ϑΟϧλϦϯά alignment/assemble

    QC ໨తผղੳ ֬ೝ࣮ݧ σʔλެ։ ࿦จ౤ߘ ϦόΠζ/௥Ճ࣮ݧ ΞΫηϓτ ҿΈձ

24. ެڞσʔλϕʔε͕ؔΘΔεςοϓ ࣮ݧσβΠϯ ༧උ࣮ݧ αϯϓϦϯά DNAௐ੔ ϥΠϒϥϦ࡞੡ γʔέϯε QC ϑΟϧλϦϯά alignment/assemble

    QC ໨తผղੳ ֬ೝ࣮ݧ σʔλެ։ ࿦จ౤ߘ ϦόΠζ/௥Ճ࣮ݧ ΞΫηϓτ ҿΈձ

25. ެڞσʔλΛར༻ͨ͠NGSݚڀͷσβΠϯ ‣ γʔέϯεલͷ࣮ݧσβΠϯ
    ‣ ྨࣅσʔλΛղੳ͢Δ͜ͱͰγʔέϯεޙͷྲྀΕΛςετ͢Δ
    ‣ γʔέϯεޙɺσʔλղੳͰ
    ‣ γʔέϯε݁Ռͷଥ౰ੑΛݕ౼͢Δ
    ‣

    ࣗલͷσʔλͱൺֱղੳΛߦ͏
    ‣ σʔλղੳޙɺ੒Ռൃදͷ৔Ͱ
    ‣ σʔλΛϨϙδτϦʹެ։͢Δ

26. ެڞσʔλͷݕࡧ͔Βղੳ·Ͱ Search, Download, and Data Analysis of Public Sequencing Data

27. ެڞσʔλͷμ΢ϯϩʔυ͔Βղੳ·Ͱ ‣ ϨϙδτϦͷݕࡧػೳͰ୳͢
    ‣ /$#*
    &#*
    %%#+ͷݕࡧΛར༻͢Δ
    ‣ σʔλͷ*%͕ࣄલʹ෼͔͍ͬͯΔ৔߹ʹ༗ޮ
    ‣

    ࿦จ΍࣬ױͳͲͷؔ࿈৘ใ͔Β୳͢
    ‣ %#$-4
    43"Λར༻͢Δ
    ‣ ެڞͷղੳαʔϏεΛར༻ͯ͠ղੳ͢Δ
    ‣ %%#+
    3FBE
    "OOPUBUJPO
    1JQFMJOF
    ‣ .VEJ
    .VUBUJPO
    %JTDPWFSZ
    JO
    ZFBTU

28. ϨϙδτϦͷݕࡧػೳͷ࢖͍ํ - github.com/inutano/sra_metadata_toolkit/wiki

29. DBCLS SRAΛར༻͢Δ - http://sra.dbcls.jp

30. DBCLS SRAΛར༻͢Δ - http://sra.dbcls.jp

31. ࿦จ͔Β୳͢ - http://sra.dbcls.jp/cgi-bin/publication.cgi

32. Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search

33. Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search

34. Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search

35. Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search

36. Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search

37. ެڞNGSղੳύΠϓϥΠϯ DDBJ Read Annotation Pipeline - http://p.ddbj.nig.ac.jp

38. ެڞNGSղੳύΠϓϥΠϯ DDBJ Read Annotation Pipeline - http://p.ddbj.nig.ac.jp

39. ࢖͍ํ͸DDBJߨशձͰ (ࢿྉ΍࿥ը΋ެ։͞Ε͍ͯ·͢) http://www.ddbj.nig.ac.jp/ddbjing/

40. Mudi: Mutation discovery in yeast - http://naoii.nig.ac.jp/mudi_top.html

41. Mudi: Mutation discovery in yeast - http://naoii.nig.ac.jp/mudi_top.html

42. Summary ‣ %#$-4ͱ౷߹%#ϓϩδΣΫτ͸ࠃ಺ͷੜ໋ՊֶϦιʔεΛ
 ੔උɾ౷߹͍ͯ͠·͢
    ‣ ެڞ%#Ͱެ։͞ΕͨσʔλΛ༗ޮʹར༻͢Δ͜ͱͰ
 ݚڀϑϩʔͷޮ཰ԽΛਤΕ·͢
    ‣ ݕࡧ΍ղੳʹެڞαʔϏεΛར༻͢Δ͜ͱͰ
 σʔλղੳͷ௿ίετԽ͕ਤΕ·͢

43. Thank you! ͝ਗ਼ௌ͋Γ͕ͱ͏͍͟͝·ͨ͠ ! t.ohta@dbcls.rois.ac.jp http://speakerdeck.com/inutano