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

NextGen Sequencing data intro.

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
Vision and LanguageからのEmbodied AIとAI for Science
Avatar for Yoshitaka Ushiku yushiku
PRO
1
400
NLP Colloquium
Avatar for Juno Kim junokim
1
180
定性データ、どう活かす？ 〜定性データのための分析基盤、はじめました〜 / How to utilize qualitative data? ~We have launched an analysis platform for qualitative data~
Avatar for 株式会社カミナシ kaminashi
7
1.1k
問いを起点に、社会と共鳴する知を育む場へ
Avatar for MATSUMOTO Ryosuke matsumoto_r
PRO
0
500
生成的推薦の人気バイアスの分析：暗記の観点から / JSAI2025
Avatar for Shotaro Ishihara upura
0
230
在庫管理のための機械学習と最適化の融合
Avatar for MIKIO KUBO mickey_kubo
3
1.1k
数理最適化と機械学習の融合
Avatar for MIKIO KUBO mickey_kubo
15
9k
最適決定木を用いた処方的価格最適化
Avatar for MIKIO KUBO mickey_kubo
4
1.8k
RHO-1: Not All Tokens Are What You Need
Avatar for Sansan R&D sansan_randd
1
160
SSII2025 [TS1] 光学・物理原理に基づく深層画像生成
Avatar for 画像センシングシンポジウム ssii
PRO
4
4k
20250624_熊本経済同友会6月例会講演
Avatar for Traffic Brain trafficbrain
1
520
データｘデジタルマップで拓く
ミラノ発・地域共創最前線
Avatar for mapconcierge mapconcierge4agu
0
200

Featured

See All Featured
Git: the NoSQL Database
Avatar for Brandon Keepers bkeepers
PRO
431
65k
The Cost Of JavaScript in 2023
Avatar for Addy Osmani addyosmani
51
8.7k
Writing Fast Ruby
Avatar for Erik Berlin sferik
628
62k
YesSQL, Process and Tooling at Scale
Avatar for Rocio Delgado rocio
173
14k
Sharpening the Axe: The Primacy of Toolmaking
Avatar for Bryan Cantrill bcantrill
44
2.4k
Creating an realtime collaboration tool: Agile Flush - .NET Oxford
Avatar for Marc Duiker marcduiker
30
2.2k
The Language of Interfaces
Avatar for Des Traynor destraynor
158
25k
How To Stay Up To Date on Web Technology
Avatar for Chris Coyier chriscoyier
790
250k
Unsuck your backbone
Avatar for Amy Palamountain ammeep
671
58k
Visualization
Avatar for Eitan Lees eitanlees
146
16k
Measuring & Analyzing Core Web Vitals
Avatar for Philip Tellis bluesmoon
7
530
Easily Structure & Communicate Ideas using Wireframe
Avatar for Afnizar Nur Ghifari afnizarnur
194
16k

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!