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Illumina

 Illumina

Intro into Illumina sequencing technology

2e0188eb9315b0ecb64537ccfe70eab8?s=128

Anton Nekrutenko

February 23, 2021
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  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