nfcore/bacass

!nf-core/bacass

A simple bacterial assembly and annotation pipeline

https://github.com/nf-core/bacass/workflows/nf-core%20CI/badge.svg](https://github.com/nf-core/bacass/workflows/nf-core%20CI/badge.svg) ![Nextflow]([***]

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 https://github.com/relipmoc/skewer and performs basic sequencing QC using FastQC. Afterwards, the pipeline performs read assembly using https://github.com/rrwick/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 https://github.com/rrwick/Porechop and assesses basic sequencing QC utilizing https://github.com/wdecoster/NanoPlot and https://github.com/a-slide/pycoQC. The pipeline can then perform long read assembly utilizing https://github.com/rrwick/Unicycler, https://github.com/lh3/miniasm in combination with https://github.com/isovic/racon or https://github.com/marbl/canu. Long reads can be polished using specified Fast5 files with https://github.com/jts/nanopolish.

Hybrid Assembly

For users specifying both short read and long read (NanoPore) data, the pipeline can perform a hybrid assembly approach utilizing https://github.com/rrwick/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 https://github.com/tseemann/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 https://github.com/andreas-wilm and is currently maintained by https://github.com/apeltzer.