nfcore/bacass repository overview

A simple bacterial assembly and annotation pipeline

⁠Introduction

⁠Short Read Assembly

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

⁠Long Read Assembly

For users that only have Nanopore data, the pipeline quality trims these using PoreChop⁠ and assesses basic sequencing QC utilizing NanoPlot⁠ and PycoQC⁠. The pipeline can then perform long read assembly utilizing Unicycler⁠, Miniasm⁠ in combination with Racon⁠ or Canu⁠. Long reads can be polished using specified Fast5 files with NanoPolish⁠.

⁠Hybrid Assembly

For users specifying both short read and long read (NanoPore) data, the pipeline can perform a hybrid assembly approach utilizing Unicycler⁠, taking the full set of information from short reads and long reads into account.

⁠Shared QC across all forms of assembly

In all cases, the assembly is assessed using QUAST⁠. The resulting bacterial assembly is furthermore annotated using Prokka⁠.

In addition, 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 computing infrastructures in a portable manner. It comes with docker or singularity containers as well as conda environments, making installation trivial and results highly reproducible.

⁠Documentation

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 config⁠
   • Reference genomes⁠
3. Running the pipeline⁠
4. Output and how to interpret the results⁠
5. Troubleshooting⁠

⁠Credits

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