Pipeline Tutorials

Follow these tutorials to learn how to use the BlobToolKit Pipeline.

Pipeline configuration

The Pipeline needs to be configured to match your local compute environment and to set parameters specific to your assembly and read data. These configuration options are set in a YAML format file before the Pipeline is run. Read more…

Running the Pipeline

The Pipeline is implemented as a Snakemake workflow that determines which jobs should be run to generate a complete BlobDir dataset based on the Pipeline configuration. The Pipeline can be run in the same way for both public and local assemblies, provided any local assembly and read files are available in the working directory. Read more…