NextGen Sequencing data intro.

Brief introduction to nextgen sequencing data.

Transcript

1. Next-Gen Sequencing Data
2. @shiondev
3. @drio
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
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)
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 …
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
54. personalize medicine
55. personalize medicine Tailor physician decisions and practices to individual patients
56. Let’s do it again for N genomes
59. Thanks!