Illumina

Intro into Illumina sequencing technology

Transcript

1. Illumina
2. Requirements ‣ Reversible termination ‣ Differentiation of nucleotides ‣ Ability to manipulate on solid support
3. Preliminary studies
4. Nucleotides Bentley et al. 2008
5. Solid support Fedurco et al. 2006
6. How it works
7. The overall idea
19. Metzker et al. 2010
20. Extending to paired ends
22. Multiplexin g
23. Some current stats (2021) illumina.com
24. Types of Illumina SBS illumina.com
25. 4 channel MiSeq illumina.com
26. 2 channel MiniSeq, NextSeq, NovaSeq illumina.com
27. 1 channel iSeq illumina.com
28. Platform Number of samples Error rate (%) Median Standard deviation MiSeq 212 0.473 0.938 MiniSeq 40 0.613 0.459 NextSeq 500 160 0.429 0.827 NextSeq 550 171 0.593 0.435 HiSeq 2500 141 0.112 0.544 NovaSeq 6000 239 0.109 0.350 HiSeq X Ten 163 0.087 0.126 Stoler 2021
29. How it does not work
30. Errors
31. Phasing and Pre-phasing
32. Illumina chastity filter
33. Sequence Specific Errors Nakamura et al. 2011
34. Schematic representation of the (a) inverted repeat and (b) enzyme preference for the SSE hypothetical mechanistic models. Nakamura K et al. Nucl. Acids Res. 2011;39:e90-e90 © The Author(s) 2011. Published by Oxford University Press.
35. A typical run Minoche et al. 2011
36. Coverage as function of GC% Minoche et al. 2011
37. Low quality bases and alignment Minoche et al. 2011
38. Goto et al. 2011
39. Context dependency Minoche et al. 2011
40. Library prep strategies
41. TrueSeq PCR-free
42. Illumina DNA Prep
43. Illumina Nextera Mate Pair
44. Illumina Nextera XT
46. Moleculo