Installation

Disclaimer

This software is not by any means production ready. It has been tested on the University of Oslo Abel cluster and on Ubuntu. It may break in spectacular ways without any warning. The author appreciates reports of successes and failures, but may not have the capacity to assist with figuring out failures.

Prerequisites

The following software is needed to run the Bifrost pipeline:

Pipeline prerequisites

• Java 7 (necessary for Nextflow.io)
• Nextflow.io

Software that the pipeline uses:

• Fastqc
• Multiqc
• bbduk.sh from the BBMap package
• Trimmomatic
• SPAdes
• BWA with the mem option
• Pilon
• QUAST
• ARIBA

Note: the software mentioned above either has to be available in the user's path, or be included as a conda environment in one of the conda config files. More information can be found on the Configuration files page.