This package contains scripts that generate color composite images from the diagnostic "Thumbnails" generated by Illumina (TM) sequencing instruments. There are slightly different recipes for compositing thumbnail images for different models of instrument.
This program first loops through a large number of black-and-white images generated by the sequencing machine of "tiles" that represent subsets of the flowcell image that are processed in batches. A 2x101 run on an Illumina hiseq produces 96 tiles x 8 flow cells x 209 cycles x 4 colors = 642,048 image files in 1672 directories.
This tool builds false-color images of the four color channels and then composities the color images of each tile into images of lanes, flowcells, and quicktime movies of the entire flowcell.
Examples of some of the output images are in the img directory.
Videos of some of our sequencing runs from 2013 can be found on youtube
And downloadable videos for teaching can be found here Flowcell directory
This package depends on python, make, imagemagick, and libav. The scripts at the moment require write access to the Thumbnails directory or a copy of it.
Thumbnail polish is under the BSD license; see LICENSE. Distribution, modification and redistribution, incorporation into other software, and pretty much everything else is allowed.
- Will Trimble (Argonne National Laboratory)
The following people
- Sarah Owens (Argonne National Laboratory) (Hiseq and Miseq)
- Scott Tighe (University of Vermont) (Hiseq)
- Zach Herbert (Dana Farber Cancer Institute) (Nextseq) have provided data and have helped interpret billions upon billions of little colored spots.
