Installation
The installation of SQUAT is very simple.
If you are getting a permission error during the installation, consider running with sudo, or create a virtual python environment.
Docker installation
hub: https://hub.docker.com/r/luke831215/squat/
docker pull luke831215/squat
docker run --name=squat_docker -it luke831215/squat
-- Running container --
git clone https://github.com/luke831215/SQUAT
cd SQUAT; make install
Github installation
Dependency
pip3 install matplotlib numpy beautifulsoup4 lxml
First, you need to clone down the repository.
git clone https://github.com/luke831215/squat
Then, go to the SQUAT directory and execute the makefile.
cd SQUAT; make install
After the installation, start running the tool with squat.sh.
Example data
For trial purposes, we extract 25000 reads from the specie Saccharomyces cerevisiae and its assembly. Run the following command to start using. See Usage and Output for more details.
./squat.sh example/SEQ.fastq -o example -r example/ASSEMBLY.fasta
After finishing, open SEQ.html in example directory to begin.