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tags:BMMB554-23
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# Lecture 16: Illumina sequencing

Illumina (originally Solexa) is the second (after 454) highly parallel sequencing technology. The original publication is [here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581791/pdf/nihms72488.pdf).

## Pros and cons

It's key advantages are:

- Reads up to 300 bp
- Paired-end sequencing is straightforward extension of the technique
- Allows multiplexing
- Relatively low error rate
- **Very high** throughput

It's main disadvantage is:

- Reads up to 300 bp

Illumina technology is by far the most widely used technology of the day:


> Screenshot taken on March 2, 2023

Although this page is no longer updated it is a good illustration of how many "seqs" were made possible by Illumina: [*"Seqs"*](https://liorpachter.wordpress.com/seq/).

## So how do it work?
<iframe src="https://docs.google.com/presentation/d/e/2PACX-1vRigKOxz8jqpZvIn9JKMQHDB-B59whz7ddn-TWuEiMY70fU5qDDTcvRt-jEsDZeYA/embed?start=false&loop=false&delayms=60000" frameborder="0" width="750" height="600" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true"></iframe>

## Let's look at Illumina data

[Illumina adata](https://colab.research.google.com/github/nekrut/BMMB554/blob/master/2023/ipynb/L15_Illumina_Q.ipynb) - looking at distribution of quality scores

## One cool application

Accuracy of Illumina sequencing can be increased with smart tagging described [here](https://www.pnas.org/content/pnas/109/36/14508.full.pdf)