Upgrade to Pro
— share decks privately, control downloads, hide ads and more …
Speaker Deck
Features
Speaker Deck
PRO
Sign in
Sign up for free
Search
Search
Public data repository and analysis pipeline fo...
Search
Tazro Inutano Ohta
July 11, 2014
Science
0
320
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
Tweet
Share
More Decks by Tazro Inutano Ohta
See All by Tazro Inutano Ohta
Yevis: System to support building a workflow registry with automated quality control
inutano
0
120
Standardization of biological sample information database
inutano
0
71
Describe data analysis workflow with workflow languages
inutano
5
5.4k
Container virtualization technologies and workflow languages improve portability and reproducibility of data analysis environment
inutano
3
340
次世代シーケンサーによるメタゲノム解析:桜の花びらに付着した環境DNAを解析する
inutano
0
100
Workflows that run everywhere and where to run them
inutano
0
160
The Sequence Read Archive search system to make use of public high-throughput sequencing data
inutano
0
290
Improve portability of bioinformatics software across HPC and cloud infrastructures
inutano
1
110
Container, Cloud, and HPC
inutano
0
170
Other Decks in Science
See All in Science
SciPyDataJapan 2025
schwalbe10
0
260
データベース11: 正規化(1/2) - 望ましくない関係スキーマ
trycycle
PRO
0
940
LayerXにおける業務の完全自動運転化に向けたAI技術活用事例 / layerx-ai-jsai2025
shimacos
2
1.5k
Agent開発フレームワークのOverviewとW&B Weaveとのインテグレーション
siyoo
0
330
Transport information Geometry: Current and Future II
lwc2017
0
180
凸最適化からDC最適化まで
santana_hammer
1
280
mathematics of indirect reciprocity
yohm
1
180
Lean4による汎化誤差評価の形式化
milano0017
1
300
🌏地球から🌌宇宙まで! 〜ケプラーの法則で繋がる天体の運動〜
syotasasaki593876
1
100
機械学習 - K近傍法 & 機械学習のお作法
trycycle
PRO
0
1.2k
How To Buy, Verified Venmo Accounts in 2025 This year
usaallshop68
3
260
データベース02: データベースの概念
trycycle
PRO
2
890
Featured
See All Featured
Producing Creativity
orderedlist
PRO
347
40k
Rebuilding a faster, lazier Slack
samanthasiow
83
9.1k
実際に使うSQLの書き方 徹底解説 / pgcon21j-tutorial
soudai
PRO
185
54k
Statistics for Hackers
jakevdp
799
220k
Git: the NoSQL Database
bkeepers
PRO
431
66k
Being A Developer After 40
akosma
90
590k
Building Adaptive Systems
keathley
43
2.7k
Thoughts on Productivity
jonyablonski
69
4.8k
What’s in a name? Adding method to the madness
productmarketing
PRO
23
3.6k
Designing Experiences People Love
moore
142
24k
Code Review Best Practice
trishagee
70
19k
Navigating Team Friction
lara
189
15k
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