Covidor

Python version

Python 3.7, 3.8, 3.9

Source

See http://github.com/sequana/covidor.

Issues

Please fill a report on github

Platform

This is currently only available for Linux distribution with bash shell (contributions are welcome to port the tool on MacOSX and other platforms)

Overview

pip install covidor

third-party tools

kraken2 and art_illumina are required for the simulation and analysis.

pip install damona
# for kraken2 only:
damona install kraken:2.0.9
# to install kraken2 and art_illumina altogether, there are both provided in the sequana_tools package:
damona install sequana_tools

Installation

For Users:

pip install covidor

For developers:

git clone git@github.com:sequana/covidor.git
cd covidor
pip install .

Testing

pytest -v ./tests

User guide and reference

• 1. User Guide
  • 1.1. Getting help
• 2. References
  • 2.1. kmer module
  • 2.2. distance module
  • 2.3. Covidor standalone (script module)