Bactopia

Introduction

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

For more information, please check:
Docker hub: https://hub.docker.com/r/bactopia/bactopia
Home page: https://github.com/bactopia/bactopia

Versions

2.0.3
2.1.1
2.2.0
3.0.0

Commands

bactopia

Module

You can load the modules by:

module load biocontainers
module load bactopia

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run bactopia on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=bactopia
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bactopia

bactopia datasets \
--ariba "vfdb_core,card" \
--species "Staphylococcus aureus" \
--include_genus \
--limit 100 \
--cpus 12

bactopia --accession SRX4563634 \
--datasets datasets/ \
--species "Staphylococcus aureus" \
--coverage 100 \
--genome_size median \
--outdir ena-single-sample \
--max_cpus 12