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Illumina Obscura


I took a picture of an Illumina plate (using QSEQ files)

Illumina sequencer output (QSEQ format) contains reads, quality scores and the X/Y coordinates from the cluster they came from.

I was curious if certain parts of an Illumina plate have lower quality reads than others. So, I decided to draw a map of an Illumina plate using these coordinates and the average quality score for that read.

In the first image, a white pixel corresponds to the presence of a sequence at a coordinate:

Black and White Illumina Photograph

You can see a subtle border between the eight lanes but not much else.

In the second image, I used two colors: Green for average quality scores above 99% (good) and Red for below (bad). This way, approximately half of the clusters are red and half are green.

Second image, in color:

Color Illumina Photograph

I did this using the Python Image Library and Python. You can see the code on GitHub.

(c) 2011-2023 Austin G. Davis-Richardson
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