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
Sequence Read Archive: Database for High-throug...
Search
Tazro Inutano Ohta
November 20, 2012
Science
0
67
Sequence Read Archive: Database for High-throughput sequencing best practice 2012
「次世代シーケンス解析と公共データベース: Sequence Read Archiveを使い倒す」
Tazro Inutano Ohta
November 20, 2012
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
100
Standardization of biological sample information database
inutano
0
54
Describe data analysis workflow with workflow languages
inutano
5
4.6k
Container virtualization technologies and workflow languages improve portability and reproducibility of data analysis environment
inutano
3
320
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
76
Workflows that run everywhere and where to run them
inutano
0
130
The Sequence Read Archive search system to make use of public high-throughput sequencing data
inutano
0
250
Improve portability of bioinformatics software across HPC and cloud infrastructures
inutano
1
94
Container, Cloud, and HPC
inutano
0
150
Other Decks in Science
See All in Science
いまAI組織が求める企画開発エンジニアとは?
roadroller
2
1.3k
Science of Scienceおよび科学計量学に関する研究論文の俯瞰可視化_LT版
hayataka88
0
990
JSol'Ex : traitement d'images solaires en Java
melix
0
120
マクロ経済学の視点で、財政健全化は必要か
ryo18cm
1
110
Snowflakeによる統合バイオインフォマティクス
ktatsuya
PRO
0
530
(論文読み)贈り物の交換による地位の競争と社会構造の変化 - 文化人類学への統計物理学的アプローチ -
__ymgc__
1
130
The Incredible Machine: Developer Productivity and the Impact of AI
tomzimmermann
0
420
【人工衛星開発】能見研究室紹介動画
02hattori11sat03
0
160
(2024) Livres, Femmes et Math
mansuy
0
110
Healthcare Innovation through Business Entrepreneurship
clintwinters
0
150
3次元点群を利用した植物の葉の自動セグメンテーションについて
kentaitakura
2
640
第61回コンピュータビジョン勉強会「BioCLIP: A Vision Foundation Model for the Tree of Life」
x_ttyszk
1
1.6k
Featured
See All Featured
Save Time (by Creating Custom Rails Generators)
garrettdimon
PRO
29
910
Docker and Python
trallard
42
3.1k
Intergalactic Javascript Robots from Outer Space
tanoku
270
27k
Producing Creativity
orderedlist
PRO
342
39k
Gamification - CAS2011
davidbonilla
80
5.1k
Building Better People: How to give real-time feedback that sticks.
wjessup
366
19k
Testing 201, or: Great Expectations
jmmastey
41
7.1k
GraphQLとの向き合い方2022年版
quramy
44
13k
Designing for Performance
lara
604
68k
BBQ
matthewcrist
85
9.4k
The Power of CSS Pseudo Elements
geoffreycrofte
73
5.4k
Chrome DevTools: State of the Union 2024 - Debugging React & Beyond
addyosmani
3
170
Transcript
࣍ੈγʔέϯεղੳͱެڞσʔλϕʔε 4FRVFODF3FBE"SDIJWFΛ͍͢ /PWBU$&3* େాୡ5B[SP0IUB ▼
ຊͷ༰ ˓ ެڞσʔλϕʔε43"4FRVFODF3FBE"SDIJWFʹ͍ͭͯ ˓ %#$-4Ͱఏڙ͍ͯ͠Δ43"ؔ࿈αʔϏε ˓ 4FRVFODF3FBE"SDIJWFϕετϓϥΫςΟε ˓ ެڞσʔλϕʔεͱ/(4ɺ՝ͱ͜Ε͔Β
ώΞϦϯά ˓ ࣍ੈγʔέϯαʔʁ ˓ 4FRVFODF3FBE"SDIJWFʁ ˓ %#$-443"ʁ
ެڞσʔλϕʔε43"4FRVFODF3FBE"SDIJWFʹ͍ͭͯ
ެڞσʔλϕʔε43"4FRVFODF3FBE"SDIJWFʹ͍ͭͯ ˓ ʹ/$#*ʹΑͬͯ/(4σʔλͷऩू͕࢝·Δ ˓ ͔Β*/4%$ʹΑΔ4FRVFODF3FBE"SDIJWFͱͯ͠ӡӦ ˓ */4%$*OUFSOBUJPOBM/VDMFPUJEF4FRVFODF%BUBCBTF$PMMBCPSBUJPO ˓ ถࠃ/$#* Ԥभ&#*
ຊ%%#+ ˓ ొडɼݕࡧμϯϩʔυͳͲΛͦΕͧΕఏڙ ˓ ొ͞Εͨσʔλަ͞ΕɼͲ͔͜ΒͰΞΫηεՄೳ
Ͳ͔͜ΒͰಉ͡σʔλʹΞΫηεՄೳ Data ID : 000001 organism : mouse cell :
nervous cell sequencer : 454 date : 2011 12 08 >Seq_Numero_1 ATGCATGCATGCATG CATGCATGCATGCAT GCATGCATGCATGCA TGCATGCATGCATGC ATGCATGCATGCATG CATGATGCATGCATG CATGCATGCATGCAT GCATGCATGCATGCA TGCATGTGCATGTGC */4%$ σʔλަ ྻσʔλ ϝλσʔλΛొ
www.ncbi.nlm.nih.gov/sra
www.ebi.ac.uk/ena
trace.ddbj.nig.ac.jp/dra
ͬͯΈΔ ˓ IVNBOCSFBTUDBODFSͷσʔλΛ୳ͯ͠ΈΔ
None
None
None
None
None
None
http://www.everystockphoto.com/photo.php?imageId=3972069
http://www.flickr.com/photos/mindaugasdanys/3766009204/ ͍ʹ͍͘
ෆຬ ˓ σʔλϕʔεͷߏ͕ෳࡶա͗Δ
σʔλ͕୳ͤͳ͍
ϛογϣϯ ˓ ެڞσʔλΛͬͱ୳͘͢͠ɼ͍͘͢͢Δ
%#$-4Ͱఏڙ͍ͯ͠Δ43"ؔ࿈αʔϏεɾπʔϧ
43"ͷσʔλΛ͍͘͢͢ΔͨΊʹ ˓ 43"ͷ֤छ౷ܭΛݩʹσʔλΛݕࡧ͢Δ ˓ ൃද͞ΕͨจΛݩʹσʔλΛݕࡧ͢Δ ˓ ࣬ױΛΩʔϫʔυʹσʔλΛݕࡧ͢Δ ˓ ొ͞ΕͨσʔλͷγʔέϯεΫΦϦςΟΛݟΔ ˓
ݕࡧ݁Ռʹؔ࿈͢ΔϝλσʔλΛޮΑ͘ϒϥδϯά͢Δ ˓ ֤43"ؔ࿈αʔϏεͷ"1*Λར༻͢Δ {@}
43"ͷ֤छ౷ܭΛݩʹσʔλΛݕࡧ͢Δ
43"ͷ֤छ౷ܭΛݩʹσʔλΛݕࡧ͢Δ ˓ ྻσʔλͱڞʹొ͞ΕΔϝλσʔλ ऍσʔλ Λूܭ ˓ γʔέϯαʔͷछྨɼαϯϓϧੜछɼ࣮ݧछΛϥϯΩϯάදࣔ ˓ σʔλొͷ৳ͼΛάϥϑͰදࣔ ͝རӹ
˓ ޮͷΑ͍ʮߜΓࠐΈݕࡧʯ ˓ ʮͲͷΑ͏ͳσʔλ͕ͲΕ͘Β͍͋Δͷ͔ʯ͕ҰͰ͔Δ ˓ ۀքͷτϨϯυΛՄࢹԽ
sra.dbcls.jp
“౷ܭ͔Β୳͢”
৳ͼͷάϥϑ
࣮ݧछผʹ৭͚
ൃද͞ΕͨจΛݩʹσʔλΛݕࡧ͢Δ
ൃද͞ΕͨจΛݩʹσʔλΛݕࡧ͢Δ ˓ 43"ͷσʔλʹจͷϦϯΫ͕ਵ͍ͯ͠ͳ͍ͷ͕ଟ͍ ˓ จ͕ग़Δલʹొ͞ΕΔσʔλ͕ଟ͍ͨΊ ˓ จݙͷத͔Βެ։σʔλͷݴٴΛநग़͠ɼ*%Λ݁ͼ͚ͭΔ ͝རӹ ˓ δϟʔφϧɼจൃද࣌ɼจλΠτϧͳͲͰιʔτͯ͠ݕࡧ
˓ ࣮ݧछɼੜछɼγʔέϯαͳͲͰߜࠐΈՄೳ
sra.dbcls.jp
“จݙ͔Β୳͢”
ߜࠐΈݕࡧ ֤ϑΟʔϧυͰฒସ͑
࣬ױΛΩʔϫʔυʹσʔλΛݕࡧ͢Δ
࣬ױΛΩʔϫʔυʹσʔλΛݕࡧ͢Δ ˓ /(4ҩֶܥͰͷར༻ଟ͍ ˓ 43"ผʹ͔Ε͍ͯͳ͍ͷͰݕࡧ͕ͮ͠Β͍ ˓ จݙʹਵ͢Δ.F4)UFSNΛݩʹσʔλΛ࣬ױͰཧ ˓ σʔλొͷଟ͍ͷɼ࣬ױͷΧςΰϦΛݩʹݕࡧՄೳ ͝རӹ
˓ .F4)ΩʔϫʔυΛݩʹ͍ͯ͠ΔͨΊਫ਼͕ߴ͍ ˓ ͰͷݚڀಈΛݟΔ͜ͱͰ͖Δ
sra.dbcls.jp
“࣬ױ͔ΒோΊΔ”
“සผ”
ొσʔλ ࣬ױؔ࿈ҨࢠDB GendooͷϦϯΫ
νΣοΫͯ͠ Search
MeSHͷؔ࿈λʔϜ ؔ࿈ʹԠͯ͡දࣔ
“࣬ױΧςΰϦผ”
πϦʔද͔ࣔΒ σʔλΛݕࡧ
ొ͞ΕͨσʔλͷγʔέϯεΫΦϦςΟΛݟΔ
ొ͞ΕͨσʔλͷγʔέϯεΫΦϦςΟΛݟΔ ˓ 43"ͷσʔλৗʹྑ͍ͷͱݶΒͳ͍ ˓ ϛεγʔέϯεొ͞Εσʔλ͕ೖ͍ͬͯΔ ˓ ͕݅ಉ͡σʔλͳΒਫ਼ͷྑ͍ͷΛ͍͍ͨ ˓ 'BTU2$ʹΑͬͯશͯͷ43"σʔλͷΫΦϦςΟΛܭࢉ ˓
IUUQXXXCJPJOGPSNBUJDTCBCSBIBNBDVLQSPKFDUTGBTURD ͝རӹ ˓ μϯϩʔυʹҰ൩͔͔ͬͨσʔλ͕յΕ͍ͯͨͱ͍͏൵ܶΛճආ ˓ γʔέϯεΫΦϦςΟͷൺֱΛ͢Δ͚ͩͰָ͍͠
g86.dbcls.jp/sra
SRA IDΛೖྗ
FastQCʹΑΔQC݁Ռ
APIʹΑΔΞΫηεՄೳ
ݕࡧ݁Ռʹؔ࿈͢ΔϝλσʔλΛޮΑ͘ϒϥδϯά͢Δ
ݕࡧ݁Ռʹؔ࿈͢ΔϝλσʔλΛޮΑ͘ϒϥδϯά͢Δ ˓ େྔͷݕࡧ݁Ռͷத͔ΒͲ͏ͬͯཉ͍͠σʔλΛݟ͚ͭग़͔͢ʁ ˓ αϯϓϧɼγʔέϯαʔͳͲͷ݅ΛൺΔ ˓ จ͕ग़͍ͯΔͷΛ༏ઌ͢Δ ˓ ݅Λൺֱ͢ΔͨΊʹɼؔ࿈͢ΔใΛͻͱ·ͱΊʹ͍ͨ͠ ͝རӹ
˓ αϯϓϧɼγʔέϯεɼϓϩδΣΫτͳͲͷ*%Ͱࠞཚ͠ͳ͍ ˓ จͷใΛซͤͯݟΔ͜ͱͰਖ਼֬ͳஅ͕Ͱ͖Δ
g86.dbcls.jp/kusarinoko
All, human, mouse, Arabidopsis ͔Βબ ΩʔϫʔυΛೖྗͯ͠ݕࡧ
จͷใ ώοτͨ͠σʔλͷϦετ
Study (project) Experiment Run (Sequence) / QC
Sample
֤43"ؔ࿈αʔϏεͷ"1*Λར༻͢Δ {@}
֤43"ؔ࿈αʔϏεͷ"1*Λར༻͢Δ ˓ ϓϩάϥϜΛͬͯ܁Γฦ͠ΞΫηε͍ͨ͠ ˓ Ұఆͷظؒ͝ͱʹಉ݅͡Ͱݕࡧ͍ͨ͠ ˓ େྔͷσʔλͷใΛݕࡧ͍ͨ͠ ͝རӹ ˓ ৗͷख͕ؒେ෯ʹݮΔ
ৗͷख͕ؒ େ෯ʹݮΔ
͝རӹ ˓ ৗͷख͕ؒେ෯ʹݮΔ
g86.dbcls.jp/sra
Sequence Quality
SRA IDม ϝλσʔλͷऔಘ
Ұ෦ͷΈެ։த ˓ ৗͷखؒΛେ෯ʹݮΒ͘͢Ӷҙ։ൃதͰ͢
4FRVFODF3FBE"SDIJWFϕετϓϥΫςΟε
ެڞγʔέϯεσʔλΛ͏खॱ ݕࡧ ϒϥδϯά μϯϩʔυ νΣοΫ ղੳ จʹهࡌ͞Εͨ*%ΩʔϫʔυͰݕࡧ ݕࡧ݁ՌΛݸผʹݟͯཉ͍͠σʔλΛ୳͢ '51"TQFSBͳͲͰσʔλΛμϯϩʔυ͢Δ μϯϩʔυͨ͠σʔλΛ֬ೝ͢Δ
ղੳʹར༻͢Δ
֤εςοϓΛޮԽίετμϯ ݕࡧ ϒϥδϯά μϯϩʔυ νΣοΫ ղੳ
ࣄલʹνΣοΫͯ͠μϯϩʔυͷίετԼ͛Δ ݕࡧ ϒϥδϯάɾνΣοΫ μϯϩʔυ ղੳ
ࣄલʹνΣοΫͯ͠μϯϩʔυͷίετԼ͛Δ ݕࡧ ϒϥδϯάɾνΣοΫ μϯϩʔυ ղੳ ౷ܭɼจɼ࣬ױɼΩʔϫʔυͰݕࡧ ݕࡧ݁Ռ͔ΒσʔλΛ୳͠ɼΫΦϦςΟ֬ೝ μϯϩʔυ
ެڞ/(4σʔλͷೋ࣍ར༻ྫ ˓ ࣗͷσʔλͱಉ݅͡ͷσʔλΛར༻ͯ͠/ΛՔ͙ ˓ ࣗͷσʔλͱؔ࿈͢ΔσʔλΛར༻͠ൺֱղੳΛߦ͏ ˓ ҟͳΔॲཧ۠ɼۙԑछɼ(FOPNF5SBOTDSJQUPNF&QJHFOPNFͳͲ ˓ ղੳπʔϧͷੑೳධՁʹར༻͢Δ ˓
ෳͷπʔϧͷൺֱɼ৽نπʔϧ։ൃ࣌ͷσϞσʔλͱͯ͠ ˓ σʔλΛେྔʹूΊͯϝλղੳΛߦ͏ ˓ੜछࡉ๔ͰԣஅతͳղੳͳͲ
43"͕ͬͱ͍͘͢ͳΓ·ͨ͠ ˓ ͜ΕͰͲΜͲΜެڞσʔλΛͬͯݚڀ͕Ͱ͖Δ
http://www.flickr.com/photos/mindaugasdanys/3766009204/ ·͍ͩʹ͍͘
ෆຬ ˓ ݕࡧ͕͍ ˓ πʔϧ͕όϥόϥͰ࿈ܞͮ͠Β͍
http://www.flickr.com/photos/66986780@N00/137720685/ վྑத
͠Β͓͍ͪͩ͘͘͞ ˓ ։ൃܧଓதɼϑΟʔυόοΫ͓͍ͪͯ͠·͢
ެڞσʔλϕʔεͱ/(4ɺ՝ͱ͜Ε͔Β
ԿނσʔλΛҰൠެ։͢Δͷ͔ ˓ ࠶ݱੑͷ୲อ ˓ ࠶ղੳͷखஈΛఏڙ͠ਖ਼ੑΛূ໌͢Δ ˓ ೋ࣍ར༻ͷଅਐ ˓ ϦιʔεΛγΣΞ͠ɼଞͷݚڀऀʹར༻ͯ͠Β͏
࣮ ˓ ग़ͤͱݴΘΕΔ͔Βग़͢ ˓ δϟʔφϧʹߘ͢Δࡍʹެڞ%#ͷ*%ΛٻΊΒΕΔ ˓ άϥϯτͷن্શͯͷσʔλΛެ։͠ͳ͚ΕͳΒͳ͍߹
http://www.flickr.com/photos/74521133@N00/232362142/ ग़͞ͳ͖Ό͍͚ͳ͍
͝རӹ͕ͳ͍ ˓ σʔλͷެ։ʹίετ͕͔͔Δ ˓ ଞਓ͕͍͍͢Α͏ʹ៉ྷʹཧ͢Δͷେม ˓ /(4σʔλαΠζ͕େ͖͍ͷͰΞοϓϩʔυ͢ΔͷҰۤ࿑ ˓ σʔλΛग़ͨ͠ਓͷϦεϖΫτ ˓
จൃදલͷσʔλΛୈࡾऀ͕ղੳͯ͠จʹʁ ˓ ݱঢ়ͰσʔλΛग़͚ͩ͢ͰۀʹͳΒͳ͍
ΞʔΧΠϒͲ͏͋Δ͖͔ ˓ σʔλެ։ͷෑډΛԼ͛Δ ˓ σʔλΛެ։͢ΔͨΊͷํ๏Λඪ४Խ͢Δ ˓ NJOJNVNJOGPSNBUJPOͳͲ ˓ ΑΓ؆୯ʹσʔλΛొ͢ΔͨΊͷΈ ˓
σʔλར༻Λଅਐ͢Δ ˓ ެ։σʔλΛΑΓ͍͘͢ཧ͢Δ ˓ ެ։σʔλΛ༗ޮར༻͢ΔͨΊͷํ๏ ˓ σʔλΛग़͢ਓʹ͝རӹΛ ˓ ެ։σʔλʹ%0*ΛৼͬͯҾ༻ΛՄೳʹ͢Δ
Ͳ͏͢Δ ˓ Ͳ͏͢Εʁ
http://www.flickr.com/photos/mindaugasdanys/3766009204/ ͕ΜΓ·͢
͝ਗ਼͋Γ͕ͱ͏͍͟͝·ͨ͠