snippy
Link to section 'Introduction' of 'snippy' Introduction
Snippy is a tool for rapid haploid variant calling and core genome alignment.
Docker hub: https://hub.docker.com/r/staphb/snippy and its home page on Github.
Link to section 'Versions' of 'snippy' Versions
- 4.6.0
Link to section 'Commands' of 'snippy' Commands
- snippy
- snippy-clean_full_aln
- snippy-core
- snippy-multi
- snippy-vcf_extract_subs
- snippy-vcf_report
- snippy-vcf_to_tab
Link to section 'Module' of 'snippy' Module
You can load the modules by:
module load biocontainers
module load snippy
Link to section 'Example job' of 'snippy' 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 Snippy on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=snippy
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers snippy