After installing, one needs to download the required databases and create a sample configuration file.
To download the databases and their respective metadata databases:
atlas download -o ~/databases
The downloads use approximately 30 GB of disk space.
To create a configuration file run:
atlas make-config --database-dir ~/databases \ config.yaml ~/directory_with_fastqs
Sample names and file paths along with default settings will populate config.yaml. This YAML file can be updated with any text editor.
Sample names should be A-Z characters and can be dash (“-“) delimited.
After editing your configuration file and adjusting any additional parameters we run assemblies across our samples using:
atlas assemble config.yaml
By default, this will write results into our current working directory across the total number of CPU cores available.