Upgrade to Pro — share decks privately, control downloads, hide ads and more …

NextGen Sequencing data intro.

Sponsored · Your Podcast. Everywhere. Effortlessly. Share. Educate. Inspire. Entertain. You do you. We'll handle the rest. →
Avatar for David Rio Deiros David Rio Deiros
March 26, 2012
Research
3
230

NextGen Sequencing data intro.

Brief introduction to nextgen sequencing data.

Avatar for David Rio Deiros

David Rio Deiros

March 26, 2012
Tweet

Other Decks in Research

See All in Research
情報技術の社会実装に向けた応用と課題：ニュースメディアの事例から / appmech-jsce 2025
Avatar for Shotaro Ishihara upura
0
310
When Learned Data Structures Meet Computer Vision
Avatar for Yusuke Matsui matsui_528
1
2.7k
Multi-Agent Large Language Models for Code Intelligence: Opportunities, Challenges, and Research Directions
Avatar for Fatemeh Fard (UBC) fatemeh_fard
0
120
HU Berlin: Industrial-Strength Natural Language Processing with spaCy and Prodigy
Avatar for Ines Montani inesmontani
PRO
0
200
令和最新技術で伝統掲示板を再構築: HonoX で作る型安全なスレッドフロート型掲示板 / かろっく@calloc134 - Hono Conference 2025
Avatar for calloc134 calloc134
0
550
自動運転におけるデータ駆動型AIに対する安全性の考え方 / Safety Engineering for Data-Driven AI in Autonomous Driving Systems
Avatar for Fuyuki Ishikawa / 石川 冬樹 ishikawafyu
0
130
Stealing LUKS Keys via TPM and UUID Spoofing in 10 Minutes - BSides 2025
Avatar for AnyKeyShik anykeyshik
0
180
説明可能な機械学習と数理最適化
Avatar for kelicht kelicht
2
920
Combining Deep Learning and Street View Imagery to Map Smallholder Crop Types
Avatar for SatAI.challenge satai
3
560
さまざまなAgent FrameworkとAIエージェントの評価
Avatar for Kento.Yamada ymd65536
1
410
姫路市 -都市OSの「再実装」-
Avatar for Hopin hopin
0
1.6k
生成的情報検索時代におけるAI利用と認知バイアス
Avatar for Y. Yamamoto trycycle
PRO
0
260

Featured

See All Featured
Helping Users Find Their Own Way: Creating Modern Search Experiences
Avatar for Dan Newman danielanewman
31
3.1k
Making the Leap to Tech Lead
Avatar for Ryan Cromwell cromwellryan
135
9.7k
The Director’s Chair: Orchestrating AI for Truly Effective Learning
Avatar for Mike Taylor tmiket
1
96
JavaScript: Past, Present, and Future - NDC Porto 2020
Avatar for David Neal reverentgeek
52
5.8k
Test your architecture with Archunit
Avatar for Yoan thirion
1
2.1k
Exploring anti-patterns in Rails
Avatar for Elle Meredith aemeredith
2
250
Side Projects
Avatar for Sacha Greif sachag
455
43k
Impact Scores and Hybrid Strategies: The future of link building
Avatar for Tamara Novitovic tamaranovitovic
0
200
Max Prin - Stacking Signals: How International SEO Comes Together (And Falls Apart)
Avatar for Tech SEO Connect techseoconnect
PRO
0
83
Ruling the World: When Life Gets Gamed
Avatar for Sebastian Deterding codingconduct
0
140
Organizational Design Perspectives: An Ontology of Organizational Design Elements
Avatar for Dr. Kim W Petersen kimpetersen
PRO
1
110
Unsuck your backbone
Avatar for Amy Palamountain ammeep
671
58k

Transcript

  1. Next-Gen Sequencing Data

  2. @shiondev

  3. @drio

  4. None

  5. Σ Bases DNA == “The Genome”

  6. Σ Bases DNA == “The Genome” 3Gbp

  7. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG…

  8. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G  

  9. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G  

  10. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G   T  

  11. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G   T   -­‐  

  12. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G   T   -­‐   A  

  13. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G   T   -­‐   A  

  14. SEQUENCING

  15. None

  16. # of Bases per day per machine

  17. 200kbp 2000

  18. 1Mbp 2003

  19. 200 Mbp 2005

  20. 3Gbp 2009

  21. 60Gbp 2012

  22. what can we do with NGS data?

  23. Re-sequencing

  24. Re-sequencing Looking for changes in a Genome

  25. Re-sequencing Looking for changes in a Genome (Given that we

    have a HIGH quality reference)

  26. Re-sequencing Looking for changes in a Genome (Given that we

    have a HIGH quality reference) Consequences?

  27. Reliably finding those changes is not easy

  28. (1%-3%) of your bases may be errors.

  29. 30x

  30. What’s the typical workflow in a re-sequencing project ?

  31. Library preparation

  32. Library preparation Sequencing

  33. Library preparation Sequencing Analysis I (images -> reads)

  34. .fastq ... >HWI-ST821_0129:5:1101:1927:2089#GATCAG/1 TGGACAACGGCCAGGTTAATGATGGGCAGGTAGAAGATGATCACT +HWI-ST821_0129:5:1101:1927:2089#GATCAG/1 ___ccccccYc[eff`]X`a^ef][RHP^_cXIYSXcXcfSWXcd ...

  35. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments)
  36. None

  37. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments) Analysis III (Variant calling)

  38. .vcf

  39. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments) Analysis III (Variant calling) Annotation

  40. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments) Analysis III (Variant calling) Annotation Science starts here …
  41. None

  42. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments) Analysis III (SNP calling) Annotation 5/15 Tb 150Gb 80G 16 8G 1G 1 400Mb 1

  43. 1 Genome (3-6 days) ~ 230Gb

  44. 1 Genome

  45. Let’s do it again for N genomes

  46. Let’s do it again for N genomes

  47. None
  48. None
  49. None
  50. None
  51. None
  52. None
  53. None

  54. personalize medicine

  55. personalize medicine Tailor physician decisions and practices to individual patients

  56. Let’s do it again for N genomes

  57. None
  58. None

  59. Thanks!