Exploring how k-mer based compression speeds up many bioinformatics applications

This is the repository where I'll store and explain my work towards the master thesis which can be found [here].

What's this thesis about?

Briefly: I used a tool called USTAR to compress genome datasets and evaluated how well this compression works in tandem with various tools.

How?

Using Singularity and a computing cluster. For more information, look into the dedicated section: Singularity.

Which tool did I use?

USTAR: GitHub page here
Fulgor: GitHub page here
GGCAT: GitHub page here
Kmdiff: GitHub page here
Mash: GitHub page here
REINDEER2: GitHub page here

A summary of all the tools' results is reported in spreadsheet foramt inside the tools folder.

Datasets

You can find info about the datasets in the datasets section.

Modify USTAR

I also modified USTAR to make it do things it wasn't capable of doing before, all the details are into this folder (I suggest reading the Singularity section beforehand)