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Public data repository and analysis pipeline fo...
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Tazro Inutano Ohta
July 11, 2014
Science
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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
Tazro Inutano Ohta
July 11, 2014
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Transcript
࣍ੈγʔέϯαʔΛར༻ͨ͠ݚڀࣄྫͱͦΕΛࢧ͑Δެڞπʔϧɾσʔλϕʔε Public data repository and analysis pipeline for high-throughput sequencing
ใɾγεςϜݚڀػߏ ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔ େా ୡ <
[email protected]
> ! prepared for ୈ186ճ ߬ࡉ๔ݚڀձ ྫձ July 11, 2014
Agenda ‣ %#$-4ͱ౷߹%#ϓϩδΣΫτʹ͍ͭͯ ‣ /(4ʹؔ࿈͢Δσʔλϕʔε ‣ /(4Λͬͨݚڀϑϩʔʹ͓͚Δެ։%#ͷׂ ‣ ެڞσʔλͷݕࡧ͔Βղੳ·Ͱ
DBCLSͱ౷߹σʔλϕʔεϓϩδΣΫτʹ͍ͭͯ Database Integration Project and DBCLS
DBCLSͱ౷߹σʔλϕʔεϓϩδΣΫτʹ͍ͭͯ ‣ େֶڞಉར༻ػؔ๏ਓใɾγεςϜݚڀػߏ 30*4 ࡿԼ ‣ +45ࡿԼͷ/#%$ ಉ͘͡30*4ࡿԼͷҨݚ%%#+ͱ࿈ܞ ‣ /#%$ϑΝϯσΟϯάɼ%%#+σʔλΞʔΧΠϒɼ%#$-4ٕज़։ൃΛ୲
ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔ %#$-4 ɺੜ໋Պֶʹ͓͚Δ σʔλެ։ͷଅਐͱσʔλϕʔεߏஙʹࢿ͢Δٕज़ͷݚڀ։ൃΛߦ͏ݚڀॴͰ͢ɻ
http://dbcls.rois.ac.jp/about
DBCLSͱ౷߹ϓϩδΣΫτ: ͜Ε·Ͱʹ։ൃɾӡ༻͖ͯͨ͠αʔϏε ‣ *OUFHCJPσʔλϕʔεΧλϩά ‣ ੜ໋ՊֶσʔλϕʔεΞʔΧΠϒ ‣ ͦͷଞɼσʔλϕʔεԣஅݕࡧͳͲ%#౷߹ʹࢿ͢ΔαʔϏε ‣ ݸผʹݚڀ։ൃΛߦ͍ͬͯΔٕज़ͷԠ༻ͱͯ͠ͷαʔϏε
‣ UPHPHFOPNF ((3/" 3FG&Y ৽ணจϨϏϡʔ ౷߹57 *O.F9FT FUD
Database of Databases: Integbio DBcatalog http://integbio.jp/dbcatalog
ੜछΧςΰϦʹΑΔߜࠐ͕Մೳ http://integbio.jp/dbcatalog
DBͷҡ࣋ɼҾ͖ड͚·͢ http://dbarchive.biosciencedbc.jp/
ҰׅDLར༻ڐཧΛαϙʔτ http://dbarchive.biosciencedbc.jp/
Find more at http://biosciencedbc.jp
togogenome.org ggrna.dbcls.jp refex.dbcls.jp first.lifesciencedb.jp togotv.dbcls.jp docman.dbcls.jp/im
togogenome.org ggrna.dbcls.jp refex.dbcls.jp first.lifesciencedb.jp togotv.dbcls.jp docman.dbcls.jp/im ήϊϜใ/ՄࢹԽ ߴԘجྻݕࡧ ҨࢠൃݱϦϑΝϨϯε ຊޠจϨϏϡʔ
ಈըνϡʔτϦΞϧ จࣥචαϙʔτ
Find more at http://dbcls.rois.ac.jp/services
NGSʹؔ࿈͢Δσʔλϕʔε Data Repositories and Databases for high-throughput sequencing
NGSʹؔ࿈͢Δσʔλϕʔεɾެ։σʔλϨϙδτϦ ‣ ࠃࡍԘجྻσʔλϕʔεͱ4FRVFODF3FBE"SDIJWF ‣ ڊେϓϩδΣΫτʹΑΔσʔλϗεςΟϯά
ࠃࡍԘجྻσʔλϕʔεͱSequence Read Archive ‣ */4%$*OU`M/VDMFPUJEF4FRVFODF%BUBCBTF$PMMBCPSBUJPO ‣ /$#* &#* %%#+ہͷ୲νʔϜ͕ڞಉͰӡ༻ ‣
4FRVFODF3FBE"SDIJWF/(4ͷͨΊͷ1SJNBSZEBUBSFQP www.insdc.org
ڊେϓϩδΣΫτʹΑΔσʔλϗεςΟϯά ‣ نͷେ͖ͳϓϩδΣΫτͰࣗΒσʔλΛެ։͢Δ߹͕͋Δ ‣ (FOPNFT1SPKFDUIUUQHFOPNFTPSH ‣ 5IF$BODFS(FOPNF"UMBT1SPKFDUIUUQUDHBEBUBODJOJIHPW ‣ &/$0%&1SPKFDUIUUQHFOPNFVDTDFEVFODPEF ‣
σʔλͷίϐʔ͕ΫϥυαʔϏε্ʹެ։͞Ε͍ͯΔ͜ͱ ‣ HFOPNFTPO"84IUUQBXTBNB[PODPNHFOPNFT
σʔλͱσʔλϕʔεͷ֊ʹ͍ͭͯ Knowledge Summarised Data Experimental Data Knowledge-base Database Primary Data
Repository Biological Information “Database”
NGSʹؔ࿈͢Δσʔλϕʔε Knowledge-base Database Primary Data Repository
NGSʹؔ࿈͢Δσʔλϕʔε Knowledge-base Database Primary Data Repository
NGSΛͬͨݚڀϑϩʔʹ͓͚Δެ։DBͷׂ The role of database for each steps of sequencing
research procedure
ҰൠతͳNGSΛ༻͍ͨݚڀϑϩʔ ࣮ݧσβΠϯ ༧උ࣮ݧ αϯϓϦϯά DNAௐ ϥΠϒϥϦ࡞ γʔέϯε QC ϑΟϧλϦϯά alignment/assemble
QC తผղੳ ֬ೝ࣮ݧ σʔλެ։ จߘ ϦόΠζ/Ճ࣮ݧ ΞΫηϓτ ҿΈձ
ެڞσʔλϕʔε͕ؔΘΔεςοϓ ࣮ݧσβΠϯ ༧උ࣮ݧ αϯϓϦϯά DNAௐ ϥΠϒϥϦ࡞ γʔέϯε QC ϑΟϧλϦϯά alignment/assemble
QC తผղੳ ֬ೝ࣮ݧ σʔλެ։ จߘ ϦόΠζ/Ճ࣮ݧ ΞΫηϓτ ҿΈձ
ެڞσʔλΛར༻ͨ͠NGSݚڀͷσβΠϯ ‣ γʔέϯεલͷ࣮ݧσβΠϯ ‣ ྨࣅσʔλΛղੳ͢Δ͜ͱͰγʔέϯεޙͷྲྀΕΛςετ͢Δ ‣ γʔέϯεޙɺσʔλղੳͰ ‣ γʔέϯε݁ՌͷଥੑΛݕ౼͢Δ ‣
ࣗલͷσʔλͱൺֱղੳΛߦ͏ ‣ σʔλղੳޙɺՌൃදͷͰ ‣ σʔλΛϨϙδτϦʹެ։͢Δ
ެڞσʔλͷݕࡧ͔Βղੳ·Ͱ Search, Download, and Data Analysis of Public Sequencing Data
ެڞσʔλͷμϯϩʔυ͔Βղੳ·Ͱ ‣ ϨϙδτϦͷݕࡧػೳͰ୳͢ ‣ /$#* &#* %%#+ͷݕࡧΛར༻͢Δ ‣ σʔλͷ*%͕ࣄલʹ͔͍ͬͯΔ߹ʹ༗ޮ ‣
จ࣬ױͳͲͷؔ࿈ใ͔Β୳͢ ‣ %#$-443"Λར༻͢Δ ‣ ެڞͷղੳαʔϏεΛར༻ͯ͠ղੳ͢Δ ‣ %%#+3FBE"OOPUBUJPO1JQFMJOF ‣ .VEJ.VUBUJPO%JTDPWFSZJOZFBTU
ϨϙδτϦͷݕࡧػೳͷ͍ํ - github.com/inutano/sra_metadata_toolkit/wiki
DBCLS SRAΛར༻͢Δ - http://sra.dbcls.jp
DBCLS SRAΛར༻͢Δ - http://sra.dbcls.jp
จ͔Β୳͢ - http://sra.dbcls.jp/cgi-bin/publication.cgi
Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search
Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search
Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search
Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search
Ωʔϫʔυશจݕࡧ - http://sra.dbcls.jp/search
ެڞNGSղੳύΠϓϥΠϯ DDBJ Read Annotation Pipeline - http://p.ddbj.nig.ac.jp
ެڞNGSղੳύΠϓϥΠϯ DDBJ Read Annotation Pipeline - http://p.ddbj.nig.ac.jp
͍ํDDBJߨशձͰ (ࢿྉըެ։͞Ε͍ͯ·͢) http://www.ddbj.nig.ac.jp/ddbjing/
Mudi: Mutation discovery in yeast - http://naoii.nig.ac.jp/mudi_top.html
Mudi: Mutation discovery in yeast - http://naoii.nig.ac.jp/mudi_top.html
Summary ‣ %#$-4ͱ౷߹%#ϓϩδΣΫτࠃͷੜ໋ՊֶϦιʔεΛ උɾ౷߹͍ͯ͠·͢ ‣ ެڞ%#Ͱެ։͞ΕͨσʔλΛ༗ޮʹར༻͢Δ͜ͱͰ ݚڀϑϩʔͷޮԽΛਤΕ·͢ ‣ ݕࡧղੳʹެڞαʔϏεΛར༻͢Δ͜ͱͰ σʔλղੳͷίετԽ͕ਤΕ·͢
Thank you! ͝ਗ਼ௌ͋Γ͕ͱ͏͍͟͝·ͨ͠ !
[email protected]
http://speakerdeck.com/inutano