BACTpipe pipeline is written in Nextflow and runs on Linux and Mac OSX systems.


In order to run BACTpipe, you need to have the following programs installed:

  • Java v8+ for Nextflow
  • Nextflow for workflow management, more specifically v21.04.0
  • Conda for installation of workflow tools
  • (Optional) A Kraken2 database if you want to classify taxonomy and gram stain to potentially improve genome annotations in the Prokka step.

Install BACTpipe

After installing all the beforementioned dependencies, BACTpipe will automatically install the software needed for the process using conda when running the pipeline.

Quick guide on how to install most tools

  1. Java v8+:
  2. Nextflow:
  3. Conda:
  4. Kraken2 database:


The repository contains a convenience script to easily download a Kraken2 DB: resources/