Illumina

Intro into Illumina sequencing technology

Transcript

1. Illumina
   

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2. Requirements
   ‣ Reversible termination
   ‣ Differentiation of nucleotides
   ‣ Ability to manipulate on solid support
   

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3. Preliminary studies
   

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4. Nucleotides
   Bentley et al. 2008
   

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5. Solid support
   Fedurco et al. 2006
   

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6. How it works
   

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7. The overall idea
   

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19. Metzker et al. 2010
    

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20. Extending to paired ends
    

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22. Multiplexin
    g
    

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23. Some current stats (2021)
    illumina.com
    

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24. Types of Illumina SBS
    illumina.com
    

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25. 4 channel
    MiSeq
    illumina.com
    

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26. 2 channel
    MiniSeq, NextSeq, NovaSeq
    illumina.com
    

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27. 1 channel
    iSeq
    illumina.com
    

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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
    

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29. How it does not work
    

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30. Errors
    

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31. Phasing and Pre-phasing
    

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32. Illumina chastity filter
    

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33. Sequence Specific Errors
    Nakamura et al. 2011
    

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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.
    

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35. A typical run
    Minoche et al. 2011
    

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36. Coverage as function of
    GC%
    Minoche et al. 2011
    

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37. Low quality bases and
    alignment
    Minoche et al. 2011
    

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38. Goto et al. 2011
    

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39. Context dependency
    Minoche et al. 2011
    

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40. Library prep strategies
    

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41. TrueSeq PCR-free
    

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42. Illumina DNA Prep
    

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43. Illumina Nextera Mate
    Pair
    

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44. Illumina Nextera XT
    

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46. Moleculo
    

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