yzhzu / bacannot

Generic pipeline for prokaryotic genome annotation

Bacterial Annotation (bacannot) Pipeline

Bacannot is an easy to use nextflow docker-based pipeline that adopts state-of-the-art software for prokaryotic genome annotation. It is a wrapper around a several tools that enables a better understanding of prokaryotic genomes. It uses:

• Prokka for generic annotation
• barrnap for rRNA prediction
• mlst for classification within multi-locus sequence types (STs)
• KofamScan for KO annotation
• KEGGDecoder for drawing KO annotation
• Nanopolish for methylation annotation
• JBrowse for genome browser production
• bedtools for annotation merging
• AMRFinderPlus and RGI for antimicrobial genes annotation
• Phigaro for prophage sequences prediction
• IslandPath-DIMOB for genomic islands prediction
• Plasmidfinder for in silico plasmid detection
• And the databases: CARD, ARGminer, PHASTER, ICEberg, Victors and VFDB

Further reading

This pipeline has two complementary pipelines (also written in nextflow) for NGS preprocessing and Genome assembly that can give the user a complete workflow for bacterial genomics analyses.

Table of contents

• Requirements
• Quickstart
• Documentation
  • Full usage
  • Usage Examples
  • Configuration File
  • Interactive and graphical execution

Requirements

• Unix-like operating system (Linux, macOS, etc)
• Java 8
• Docker
  • fmalmeida/bacannot:{latest, kofamscan, jbrowse, renv}

This images have been kept separate to not create massive Docker image and to avoid dependencies conflicts.

Quickstart

1. If you don't have it already install Docker in your computer. Read more here.

   • You can give this in-house script a try.

   • After installed, you need to download the required Docker images

     docker pull fmalmeida/bacannot:latest
     docker pull fmalmeida/bacannot:kofamscan
     docker pull fmalmeida/bacannot:jbrowse
     docker pull fmalmeida/bacannot:renv
     

   • Each image can be built by using the Dockerfiles in the docker folder

     cd docker
     docker build -t fmalmeida/bacannot -f Dockerfile_bacannot .
     docker build -t fmalmeida/kofamscan -f Dockerfile_kofamscan .
     docker build -t fmalmeida/jbrowse -f Dockerfile_jbrowse .
     docker build -t fmalmeida/renv -f Dockerfile_renv .
     

Each release is accompanied by a Dockerfile in the docker folder. When using releases older releases, users can create the correct image using the Dockerfile that goes alongside with the release (Remember to give the image the correct name, as it is in dockerhub and the nextflow script). The latest release will always have its docker image in dockerhub.

2. Install Nextflow (version 20.07 or higher):

   curl -s https://get.nextflow.io | bash
   

3. Give it a try:

   nextflow run fmalmeida/bacannot --help
   

Users can get let the pipeline always updated with: nextflow pull fmalmeida/bacannot

Documentation

Usage

• Complete command line explanation of parameters:
  • nextflow run fmalmeida/bacannot --help
• See usage examples in the command line:
  • nextflow run fmalmeida/bacannot --examples
• However, users are encouraged to read the complete online documentation.

Command line usage examples

Command line executions are exemplified in the manual.

Using the configuration file

All the parameters showed above can be, and are advised to be, set through the configuration file. When a configuration file is set the pipeline is run by simply executing nextflow run fmalmeida/bacannot -c ./configuration-file

Your configuration file is what will tell to the pipeline the type of data you have, and which processes to execute. Therefore, it needs to be correctly set up.

Create a configuration file in your working directory:

  nextflow run fmalmeida/bacannot --get_config

Interactive graphical configuration and execution

Users can trigger a graphical and interactive pipeline configuration and execution by using nf-core launch utility.

Install nf-core

# Install nf-core
pip install nf-core

launch the pipeline

nf-core launch will start an interactive form in your web browser or command line so you can configure the pipeline step by step and start the execution of the pipeline in the end.

# Launch the pipeline
nf-core launch fmalmeida/bacannot

It will result in the following:

nextflow tower

This pipeline also accepts that users track its execution of processes via nextflow tower. For that users will have to use the parameters --use_tower and --tower_token.

Citation

Please cite this pipeline using our Zenodo tag or directly via the github url. Also, whenever used/helpful, remember to cite the following software:

• Prokka for generic annotation
• barrnap for rRNA prediction
• mlst for classification within multi-locus sequence types (STs)
• KofamScan for KO annotation
• KEGGDecoder for drawing KO annotation
• Nanopolish for methylation annotation
• JBrowse for genome browser production
• bedtools for annotation merging
• AMRFinderPlus and RGI for antimicrobial genes annotation
• Phigaro for prophage sequences prediction
• IslandPath-DIMOB for genomic islands prediction
• Plasmidfinder for in silico plasmid detection
• And the databases: CARD, ARGminer, PHASTER, ICEberg, Victors and VFDB