Intro into Illumina sequencing technology
Illumina
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Requirements‣ Reversible termination‣ Differentiation of nucleotides‣ Ability to manipulate on solid support
Preliminary studies
NucleotidesBentley et al. 2008
Solid supportFedurco et al. 2006
How it works
The overall idea
Metzker et al. 2010
Extending to paired ends
Multiplexing
Some current stats (2021)illumina.com
Types of Illumina SBSillumina.com
4 channelMiSeqillumina.com
2 channelMiniSeq, NextSeq, NovaSeqillumina.com
1 channeliSeqillumina.com
Platform Number of samplesError rate (%)MedianStandarddeviationMiSeq 212 0.473 0.938MiniSeq 40 0.613 0.459NextSeq 500 160 0.429 0.827NextSeq 550 171 0.593 0.435HiSeq 2500 141 0.112 0.544NovaSeq 6000 239 0.109 0.350HiSeq X Ten 163 0.087 0.126Stoler 2021
How it does not work
Errors
Phasing and Pre-phasing
Illumina chastity filter
Sequence Specific ErrorsNakamura et al. 2011
Schematic representation of the (a) inverted repeat and (b) enzyme preference for the SSEhypothetical mechanistic models.Nakamura K et al. Nucl. Acids Res. 2011;39:e90-e90© The Author(s) 2011. Published by Oxford University Press.
A typical runMinoche et al. 2011
Coverage as function ofGC%Minoche et al. 2011
Low quality bases andalignmentMinoche et al. 2011
Goto et al. 2011
Context dependencyMinoche et al. 2011
Library prep strategies
TrueSeq PCR-free
Illumina DNA Prep
Illumina Nextera MatePair
Illumina Nextera XT
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