Three commands to start analysing your metagenome data:
conda install -c bioconda -c conda-forge metagenome-atlas atlas init --db-dir databases path/to/fastq/files atlas run
All databases and dependencies are installed on the fly in the directory
You want to run this three commands on the example_data on the GitHub repo.
If you have more time, then we recommend you to configure atlas according to your needs:
.. toctree:: :maxdepth: 1 :caption: Setup usage/getting_started usage/cluster usage/test
.. toctree:: :maxdepth: 2 :caption: The Pipeline details/pipeline details/configuration