Illumina

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

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19. Metzker et al. 2010

20. Extending to paired ends

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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

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46. Moleculo