cello2

3d semester, biotechnology seminar: cello-2 practice

Students:

• Maria Firulyova
• Elizaveta Grigoryeva

Tutor: Alexander Tkachenko

Master's program webpage: https://ctlab.itmo.ru/bioinf-master/

Installation

To run the pipeline, install cello-2 with all prerequisites:

• Link to the installation instructions
• Snakemake

Config structure

After installation, fill the config.yaml file with your pathes:

• app_path -- path to the cello2-jar file
• data_path -- path with json input data
• logic_path -- path with logic files
• targets -- basename(s) of target files (unique prefixes for UCF files in data_path folder)

Pipeline structure

Execution

snakemake --cores 2

Results

Check output/target/logic folders for results, e.g., if target was SC1C1G1T1 and logic was xor, check output/SC1C1G1T1/xor.v folder.

References

• Article: https://www.nature.com/articles/s41564-020-0757-2
• Useful explanation: link