This pipeline is for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using Skewer and performs basic QC using FastQC. Afterwards, the pipeline performs read assembly using Unicycler and assesses assembly quality using QUAST. Contamination of the assembly is checked using Kraken2 to verify sample purity. The resulting bacterial assembly is annotated using Prokka.

Furthermore, the pipeline creates various reports in the results directory specified, including a MultiQC report summarizing some of the findings and software versions.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.


The nf-core/bacass pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting


nf-core/bacass was originally written by Andreas Wilm and is currently maintained by Alexander Peltzer.