bactopia
Link to section 'Introduction' of '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!
Docker hub: https://hub.docker.com/r/bactopia/bactopia
Home page: https://github.com/bactopia/bactopia
Link to section 'Versions' of 'bactopia' Versions
- 2.0.3
- 2.2.0
Link to section 'Commands' of 'bactopia' Commands
- bactopia
Link to section 'Module' of 'bactopia' Module
You can load the modules by:
module load biocontainers
module load bactopia
Link to section 'Example job' of 'bactopia' Example job
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