Getting Started

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.

Configuration File

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.