Public data repository and analysis pipeline for high-throughput sequencing

特定非営利活動法人酵母細胞研究会 第186回例会 次世代シーケンサーを活用した研究事例と、それを支える公共ツール・データベース

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