shovill
Link to section 'Introduction' of 'shovill' Introduction
Shovill is a tool to assemble bacterial isolate genomes from Illumina paired-end reads.
Docker hub: https://hub.docker.com/r/staphb/shovill
Home page: https://github.com/tseemann/shovill
Link to section 'Versions' of 'shovill' Versions
- 1.1.0
Link to section 'Commands' of 'shovill' Commands
- shovill
Link to section 'Module' of 'shovill' Module
You can load the modules by:
module load biocontainers
module load shovill
Link to section 'Example job' of 'shovill' 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 shovill on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=shovill
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers shovill
shovill --outdir out \
--R1 test/R1.fq.gz \
--R2 test/R2.fq.gz