Basic analysis
Principal component analysis (PCA)
To use Circula, first install it using pip or conda:
$ pip install circula
OR
$ conda install -c conda-forge circula
Differential analysis
To initialize a Circula program, use the circula init command. This command will create a new Circula project in the specified directory. The -r flag is required to specify the reference genome. The --ref-index and --ref-dict flags are optional and will create the reference genome index and dictionary files, respectively. --ref-index and --ref-dict flags are required for the alignment step and can be skipped if the reference genome index and dictionary files are already available at the directory enclosing the reference genome.
circula init -r ${reference} --ref-index --ref-dict -o ./project_dir