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
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
Search
Tazro Inutano Ohta
December 26, 2018
Education
0
64
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
JSTグローバルサイエンスキャンパス事業
「医学・医療の学際的修学、半学半教」プログラム
於 慶應義塾大学日吉キャンパス
Tazro Inutano Ohta
December 26, 2018
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
96
Standardization of biological sample information database
inutano
0
41
Describe data analysis workflow with workflow languages
inutano
4
3.8k
Container virtualization technologies and workflow languages improve portability and reproducibility of data analysis environment
inutano
3
320
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
220
Improve portability of bioinformatics software across HPC and cloud infrastructures
inutano
1
83
Container, Cloud, and HPC
inutano
0
140
shell-vs-genome
inutano
0
750
Other Decks in Education
See All in Education
Microsoft Office 365
matleenalaakso
0
1.5k
phygital__le_magasin_augmenté.pdf
martine
0
2.6k
Educación digital en la adolescencia
gonz1ale1
0
100
Canva
matleenalaakso
0
170
Switches
irocho
0
200
情報Iの「縦糸」と「横糸」を意識したプログラム教育の実践
asial_edu
0
220
Introduction - Lecture 1 - Next Generation User Interfaces (4018166FNR)
signer
PRO
0
3.1k
Digijulkaisut
matleenalaakso
1
8.6k
TCA Practice in 5 min
d_date
1
640
Implicit and Cross-Device Interaction - Lecture 10 - Next Generation User Interfaces (4018166FNR)
signer
PRO
1
1.2k
Design Guidelines and Principles - Lecture 7 - Information Visualisation (4019538FNR)
signer
PRO
0
1.7k
経験に複利を効かせろ!ふりかえり研修2024
pokotyamu
22
8k
Featured
See All Featured
Documentation Writing (for coders)
carmenintech
60
4k
The Mythical Team-Month
searls
217
42k
10 Git Anti Patterns You Should be Aware of
lemiorhan
649
58k
Bash Introduction
62gerente
605
210k
Debugging Ruby Performance
tmm1
70
11k
Fashionably flexible responsive web design (full day workshop)
malarkey
398
65k
Git: the NoSQL Database
bkeepers
PRO
423
63k
KATA
mclloyd
16
12k
Infographics Made Easy
chrislema
238
18k
Navigating Team Friction
lara
179
13k
Sharpening the Axe: The Primacy of Toolmaking
bcantrill
22
1.4k
Principles of Awesome APIs and How to Build Them.
keavy
121
16k
Transcript
DNA (DBCLS) 2018/12/26 JST
!
"#
ࠓͷ͓ ੜֶNFBUTใՊֶ
http://docman.dbcls.jp/im/
None
ٕज़ͷਐา͕ή ϊϜՊֶͷઓུΛม͑ͨ ͝Ζ
Ή͔͠αϯΨʔ๏ʹΑΔ%/"ྻղಡ Ͱ͖Δ͜ͱ͔Βͭͭ͜͜ͱ
͜ΕΛઃܭ͠ͳ͍ͱಡΊͳ͍ ग़య: https://www.researchgate.net/figure/Principle‐of‐Sanger‐sequencing‐Incorporation‐of‐ ddNTPs‐terminates‐the‐elongation‐of‐the_fig4_265264877
͍·େنԘجྻղಡٕज़ʹΑΔཏతܭଌ ͱΓ͋͑ͣશ෦ಡΉ
ͿͭΓʹ͢Δ શ෦ʹΞμϓλʔྻΛ͚ͭΔ શͯͷྻʹରͯ͠ ૬ิͷ߹Λ͢Δ ೋ࣍ݩ্ۭؒͷܬޫΛ ΧϝϥͰࡱӨɺܦ࣌ͷ มԽΛॲཧͯ͠ྻʹ ม͢Δ ग़య: https://bitesizebio.com/13546/sequencing‐by‐synthesis‐explaining‐the‐illumina‐sequencing‐technology/
ಡΊͳ͔ͬͨͷ͕ಡΊΔΑ͏ʹ ͱΓ͋͑ͣಡΜͰΈΑʂ
ग़య: https://gold.jgi.doe.gov/statistics
͋ͷੜͷή ϊϜͬͯ͏ಡ·Ε͚ͯͨͬʁ ή ϊϜหϓϩδΣΫτ
ग़య: https://www.instagram.com/p/BcybbydAbSK/
ग़య: http://wiki.lifesciencedb.jp/mw/GenomeBentoProject
େྔฒྻΛ༷ͬͯʑͳݱΛܭଌ͢Δ 4FRͷ࣌
ϥϘ͔Βσʔλ͕ͲΜͲΜग़ͯ͘Δ ͕ͩγʔέϯαੜମࢠΛจࣈʹม͢ΔػցͰ͋ΓࣝΛੜΉͷͰͳ͍
None
ੜֶͷࣝ ใՊֶͷٕज़Ͱ จࣈྻͷฒͼΛࣝʹม͢Δ
#JH%BUB4DJFODFͱͳͬͨੜֶܭࢉػͳ͠Ͱ͍͚ͬͯͳ͍ ੜֶNFBUTใՊֶ
Պֶతख๏ͷͭͷύϥμΠϜ ܦݧཧܭࢉσʔλ
Ծઆ͔Β࣮ݧΛσβΠϯ͢ΔPS·ͣσʔλΛऔͬͯੳ͢Δ Ծઆۦಈܕσʔλۦಈܕ
ϝλή ϊϜ Կ͕ೖͬͯΔ͔Θ͔Μͳ͍͚Ͳ%/"શ෦ಡΊΑ͘Ͷʁ
ւਫதͷ%/"͔ΒڕͷछྨΛਪఆ ͷਫશ෦ಡΉ ग़య: https://doi.org/10.1098/rsos.150088-9
ۭؾதͷ%/"͔ΒඍੜΛਪఆ ۭؾಡΉ ग़య: https://doi.org/10.1371/journal.pone.0001862
ެڞۭؒͷ%/"͔ΒඍੜΛਪఆ .FUB46#1SPKFDU ग़య: https://doi.org/10.1186/s40168‐016‐0168‐z
ഉᔔதͷ%/"͔ΒࡉەΛਪఆ ʜ͕Α͘ߦΘΕΔ͕ԼͷਤੜಈΛই͚ͭͣʹ%/"Λ࠾औ͢Δख๏ͷจ ग़య: https://doi.org/10.1038/s41598-018-20427-9
ౙɾॴ ݚڀूձʮୈ࢛ճ/(4ݱͷձʯاըձٞ
ʮ͜Ε͚ͩγʔέϯε҆͘ͳͬͨΜ͔ͩΒͳΜ͔ಡ·ͳ͍ʁʯ
None
ࡩͷछͰ͋ΔιϝΠϤγϊ͗Ͱ૿͑ΔΫϩʔϯ Ұఆͷؾ݅ͰҰ੪։Ֆ͢Δ͕Ұि͔ؒΒेͰࢄͬͯ͠·͏
॓ओͷή ϊϜಉ͡Ͱڥ͚͕݅ͩҟͳΔ ணͨ͠%/"ͷҧ͍ڥͷҧ͍Λө͢Δ͔ʁ
ͱ͍͑ҋӢʹγʔέϯε͢ΕΑ͍ͱ͍͏Θ͚Ͱͳ͍ͷͰ ݚڀσβΠϯ Λ͠·͢
༧ࢉΈ αϯϓϦϯάΩοτͱࢼༀͷௐୡ αϯϓϦϯάΛ͢Δ αϯϓϧ͔Β%/"Λநग़͢Δ 4S3/"ྖҬΛ૿෯ͯ͠γʔέϯε͢Δ ੜྨσʔλϕʔεʹ͍߹ΘͤͯಡΜͩྻ͔ΒੜछΛਪఆ͢Δ ֶձͰղੳίϯϖςΟγϣϯΛΔ จΛॻ͘
Ϋϥυιʔγϯά શࠃ͔ΒࢀՃऀΛืͬͯαϯϓϦϯάΛ͓ئ͍͢Δ
None
༧ࢉΈ αϯϓϦϯάΩοτͱࢼༀͷௐୡ ΣϒΞϓϦέʔγϣϯͷ࣮ͱެ։ એͱࢀՃऀืू ΩοτΛࢀՃऀʹૹΔ αϯϓϦϯάͯ͠Β͏ αϯϓϧΛૹͬͯΒ͏ αϯϓϧใΛॻ͍ͯొͯ͠Β͏ ૹΒΕ͖ͯͨαϯϓϧ͔Β%/"Λநग़͢Δ 4S3/"ྖҬΛ૿෯ͯ͠γʔέϯε͢Δ
ੜྨσʔλϕʔεʹ͍߹ΘͤͯಡΜͩྻ͔ΒੜछΛਪఆ͢Δ ֶձͰղੳίϯϖςΟγϣϯΛΔ จΛॻ͘
αϯϓϦϯάࢀՃऀ 149 ໊
ू·ͬͨαϯϓϧ 594
None
શࠃ੍ (ԭೄΛআ͘)
ಡΜͰΈͨ
ಘΒΕͨྻͷ΄ͱΜͲ͕ ༿ମͱϛτίϯυϦΞ ίϯλϛͩ
ίϯλϛ $POUBNJOBUJPOԚછ Պֶ࣮ݧҰൠʹ͓͍ͯҙਤ͠ͳ͍࣭͕ࠞೖ͢Δ͜ͱ
ɾТɾʆ Ұൃউෛͩͱ͜͏͍͏͜ͱ͋Δ
αϯϓϦϯά࣌ʹՖͼΒͷද໘Λ ࡲΓ͗ͯ͢ࡩͷࡉ๔͕ࠞೖͨ͠ͱ ࢥΘΕΔͷਤ
࡞ઓมߋ ݟ͔ͭͬͨྻͷதʹԿ͔໘ന͍ͷͳ͍͔ʁ
΄ͱΜͲ༿ମͱϛτίϯυϦΞ·ΈΕ ΄΅ίϯλϛͱ૾͞ΕΔ͕ɺશ෦͕ͦ͏ͳͷ͔ʁ
ҧ͏২ʹ༝དྷ͢ΔͱࢥΘΕΔྻ γʔέϯεͷϛεͷՄೳੑ͋Δ͕ɺϛεϚονͷΛߟ͑Δͱʜʁ
Cryptomeria japonica Ֆ࣌ӍࡩࢄΓΏͦ͘ͷલʹ
ɾТɾʆ ͜͏ͯ͜͠ͷੈքʹ·ͨҰͭ৽ͨͳτϦϏΞ͕ੜ·Εͨʜ
None
رͳ͍ͷ͔ ͜ͷ··Ͱকདྷʹͭͳ͕Βͳ͍
ܚጯٛक़େֶઌੜ໋Պֶݚڀॴ ߥάϧʔϓ ߥ Տ ౻ݪ ٢ా ߴҪ Ѩ෦ ࠤ౻ণ͞Μ
ٕज़һ ٕज़һ ֶੜ ॿڭ ॿڭ ॿڭ ।ڭत ൿॻ 0 50
100 150 200 count abe Arakawa Fujiwara Ishii Kono sato Takai Yoshida member * * εʔύʔςΫχγϟϯҰਓউͪ ݸਓຖͷαϯϓϦϯάʹ͓͚ΔόΫςϦΞྻ ߥ͞Μ ܚጯٛक़େ
0 1000 2000 3000 count abe Arakawa Fujiwara Ishii Kono
sato Takai Yoshida member 0 50 100 150 200 count abe Arakawa Fujiwara Ishii Kono sato Takai Yoshida member ٕज़һ ٕज़һ ֶ ॿڭ ॿ ॿڭ ।ڭत ൿॻ ٕज़һ ٕज़һ ֶ ॿڭ ॿ ॿڭ ।ڭत ൿॻ ༿ମɾϛτίϯυϦΞআ֎ ༿ମɾϛτίϯυϦΞؚΉ ՖคΛଟ͘ͱͬͯ͠·͍ͬͯΔ όΫςϦΞΛ༏ઌతʹͱΕ͍ͯΔਓ͕͍Δ 10 15 20 25 30 35 40 45 50 55 4 500 1000 1500 2000 2500 17 20 40 60 80 100 4 0 500 1000 1500 2000 2500 3000 17 0 10 20 30 40 50 4 0 250 500 750 1000 1250 1500 17 0 10 20 30 40 50 4 0 250 500 750 1000 1250 1500 17 0 5 10 15 20 25 30 4 200 400 600 800 1000 1200 1400 17 0 5 10 15 20 4 0 200 400 600 800 1000 1200 17 0 50 100 150 200 4 1500 1750 2000 2250 2500 2750 3000 17 0 20 40 60 80 100 120 4 0 500 1000 1500 2000 17 ٕज़һ ٕज़һ ֶੜ ॿڭ ॿڭ ॿڭ ।ڭत ൿॻ ༿ମɾϛτίϯυϦΞͷྻͱόΫςϦΞͷྻͷ૬ؔ ߥ͞Μ ܚጯٛक़େ
ྻσʔλɺϝλσʔλɺจͦͷଞશ෦͜͜ʹ͋Γ·͢ EBUBECDMTKQdJOVUBOPPNHTFR
αϯϓϦϯάͷख๏Λ͢ΕΑΓΑ͍σʔλ͕ಘΒΕΔ ͔ SF͓ՖݟϓϩδΣΫτ ٻΉϓϩδΣΫτϦʔμʔ
Պֶݚڀͱཱͯͤ͠͞Δ͜ͱ͚ͩͰͳ͍ ͓ՖݟϓϩδΣΫτਅͷత
༧ࢉΈ αϯϓϦϯάΩοτͱࢼༀͷௐୡ ΣϒΞϓϦέʔγϣϯͷ࣮ͱެ։ એͱࢀՃऀืू ΩοτΛࢀՃऀʹૹΔ αϯϓϦϯάͯ͠Β͏ αϯϓϧΛૹͬͯΒ͏ αϯϓϧใΛॻ͍ͯొͯ͠Β͏ ૹΒΕ͖ͯͨαϯϓϧ͔Β%/"Λநग़͢Δ 4S3/"ྖҬΛ૿෯ͯ͠γʔέϯε͢Δ
ੜྨσʔλϕʔεʹ͍߹ΘͤͯಡΜͩྻ͔ΒੜछΛਪఆ͢Δ ֶձͰղੳίϯϖςΟγϣϯΛΔ จΛॻ͘
$
None
None
࣌ΣϒΞϓϦέʔγϣϯ͕ࣗಈೖྗ αϯϓϦϯάͷॴ Ңܦߴ (14Ͱࣗಈೖྗ ఱީ࣌ͱ(14ใΛݩʹؾி%#͔Βநग़ͯࣗ͠ಈิ ։Ֆޙͷ࣌ͱ(14ใ͔Βಉ͘͡ࡩ։ՖใΑΓࣗಈิ ͦͷଞͷใࣗ༝هड़
ϓϩͷݚڀैࣄऀ͕ಉ͡ରʹ͍ͭͯௐΔ ؍ͱهड़ͷ࣭ͱྔ
ඈௗࢁଆ ࢪઃೖΓޱ ࢪઃෑ JRԦࢠӺଆ ύʔΫαΠυ λϫʔαΠυ ιϝΠϤγϊ ಓ࿏Ԋ͍ೖΓޱ ߴ80.5m αΫϥͷՖ1ݸ
ιϝΠϤγϊݩ $BTFT4JNQMFUFSNTPOMZ ղऍ͍͕͠ɺػց͕ಡΊΔ
000353(ը૾000353_1)ʹ͍ͭͯɻ000361ͱͷ૬ҧ:ڳߴܘ56cmɻथߴ10.02m(ը૾000353_2தஈ)ɻथྸ͓Α ͼ২ޙͷ͕ߴ͍ͱਪఆ͞Ε·͢ɻը૾ڳߴ෦ҎԼͷथൽ্ͷணੜ২ͷඃ෴80%ɻணੜ২ϋ ϦΨωΰέՊͳͲ᥌ଽྨ,ϊΩγϊϒͳͲ༽ࣃྨ,ϝϊΩΰέϨϓϥΰέͳͲҥମ͕ओͰɺΩϊίྨݟͨ Γ·ͤΜͰͨ͠(ը૾000353_3)ɻৗ༿थΛओͱ͢Δೋ࣍ྛ·ͨεεΩ͔Βͷڑ21mɻ000353ͱ 000361ͷڞ௨:ՖͷܗଶͷΈ͔ΒιϝΠϤγϊͱஅ͠·͕ͨ͠,ͰެԂͳͲʹ͍ΘΏΔατβΫϥͷෳ छΛࠞ২͢Δ͜ͱ͕͋ΔͷͰ,ՄೳͰ͋Εը૾(000353_4)͔Βछͷ֬ೝΛ͓ئ͍͠·͢ɻࢼྉ࠾औࣛࣇ ౡࢢɻḈຎౡ౦ଆͷࣛࣇౡʹ໘͠ɺՐࡅྲྀग़͕ଯੵͯ͠Ͱ্͖ͨϊݪ্ɻඪߴ90mɻ1978ʹ ͞Εͨॅ֎ԑͷެԂʹ২͞Εͨݸମɻ২ͷެԂͷ౦ଆͱଆʹंಓΛִͯͯ,֓Ͷೋ֊ՈҰށݐ ͯͷॅ͕͋Γ·͢ɻ૬ରর100%ɻंಓ͓ΑͼंಓԊ͍ͷ֗౮͔Βͷڑ΄΅ಉ͡ɻࣛࣇౡํؾ ۙͷԹྔࢦ140લޙɻௐࠪඪߴ͕80mఔߴ͍ͷͰͦΕΑΓΘ͔ͣʹ͍ͱߟ͑ΒΕ·͢ɻஆԹଳͷর༿
थྛଳʹ૬͠·͕͢,ஆԹଳͷর༿थྛଳʹ૬͠·͕͢,২ͷެԂͷೆଆͷࣼ30°ͷ֑ͷࣼ໘ʹৗ ༿थΛओͱ͢Δೋ࣍ྛ·͕ͨଘ͍ͯ͠Δ͚ͩͰ͢ɻ࿈׆ൃʹՐ͍ͯ͠ΔࡩౡতՐޱ͔Βͷڑ ͓Αͦ15kmɻ෩͖ʹΑͬͯ߱փ͕͋Γ·͢ɻҰൠʹࣛࣇౡपลͰۭத࣪ͷߴ͞ͱՐࢁփͷணʹΑΓ थͷװʹணੜ২͕ੜҭ͍͕͋͢͠Γ·͢ɻαϯϓϧͷՖห্ʹՐࢁփ͋Δ͍ԫ࠭ͱࢥΘΕΔԚΕ͕ ΈΒΕ·͢ɻҰൠతʹ,Ұ੪ʹ࡙͍ͯҰ੪ʹࢄΔؔ౦ͱൺΔͱ,Ͱ1ຊͷथͷ։Ֆظ͕͍ؒ(ݸʑͷՖ͕ॱ ࡙͍࣍ͯ,ॱ࣍ࢄΔ)͕͋ΔΑ͏Ͱ͢ɻ্هͷ։ՖޙͷαϯϓϦϯάͨ͠ʮՖʯͷ։ՖͰ͢ɻҢܦ ʹ͍ͭͯGPSઐ༻ػͷใ(ը૾000353_2Լஈ)Λೖྗ͠·ͨ͠ɻ $BTFJOEFUBJM ྔଟ͍͕ɺػցՄಡੑ͍
None
هड़ͷίετWTղੳ࣌ͷॊೈੑ ϝλσʔλͷ࣭ͷ্͕EBUBESJWFOTDJFODFͷ伴ΛѲ͍ͬͯΔ
• ܭଌٕज़ͷਐา͕Պֶͷख๏Λม͑Δ • σʔλۦಈܕՊֶͱͳͬͨੜֶܭࢉػՊֶͱ༥߹͢Δ • ੵͨ͠σʔλ͕ҖྗΛൃش͢Δ࣌ͦ͜σʔλͷهड़͕ॏཁ • ͍͔ʹ࣭ͷߴ͍σʔλΛऩू͢Δ͔ %
Պֶͱهड़͢Δ͜ͱ ॻ͖ͱͲΊΑɻٞͨ͜͠ͱ෩ͷதʹਧ͖ඈ͍͚ͯ͠ͳ͍
& ୈ࢛ճNGSݱͷձ اըνʔϜ ͓ՖݟϓϩδΣΫτࢀՃऀͷΈͳ͞· ຊͷσʔλϕʔεΛࢧ͑Δ DBCLS/NBDC/DDBJ ͷΈͳ͞· Bio OSSίϛϡχςΟ BioHackathon/SPARQLthon/PitagoraNetwork
ͷΈͳ͞·
' • ྻղੳͷڭՊॻతͳॻ੶ • Dr. Bonoͷੜ໋Պֶσʔλղੳ (ϝσΟΧϧαΠΤϯε Πϯλʔφγϣφϧ) • NGSͷ࣮ݧख๏ղੳͷํ๏ʹ͍ͭͯΔͨΊͷॻ੶
• ࣍ੈγʔΫΤϯεղੳελϯμʔυʙNGSͷϙςϯ γϟϧΛ׆͔͖͠ΔWET&DRY (༽ࣾ) • ౷ܭػցֶशͷଆ໘͔ΒόΠΦΠϯϑΥϚςΟΫεΛ Γ͍ͨਓ͚ • ੜ໋ใॲཧʹ͓͚Δػցֶश ଟॏݕఆͱਪఆྔઃܭ (ػցֶशϓϩϑΣογϣφϧγϦʔζ) (ߨஊࣾ) • ࠷৽ͷݚڀൃදߨԋΛYouTubeͰݟΔ • ౷߹TV http://togotv.dbcls.jp/ja/lecture.html • εϥΠυ • speakerdeck.com/inutano