Simple bacterial assembly and annotation pipeline

This pipeline is for bacterial assembly of next-gen sequencing reads. It quality-trims your reads, runs QC, including a metagenomics classifier on your reads to check for purity, assembles the reads with Unicycler, annotates the assembly with Prokka and runs Quast on the assembly for quality check.

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 / singularity 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
   • Local installation
   • Adding your own system
   • Reference genomes
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

nf-core/bacass was originally written by Andreas Wilm.