soapdenovo2
Link to section 'Introduction' of 'soapdenovo2' Introduction
Soapdenovo2 is a short-read assembly method to build de novo draft assembly.
For more information, please check its website: https://biocontainers.pro/tools/soapdenovo2.
Link to section 'Versions' of 'soapdenovo2' Versions
- 2.40
Link to section 'Commands' of 'soapdenovo2' Commands
- SOAPdenovo-127mer
- SOAPdenovo-63mer
Link to section 'Module' of 'soapdenovo2' Module
You can load the modules by:
module load biocontainers
module load soapdenovo2
Link to section 'Example job' of 'soapdenovo2' 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 Soapdenovo2 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=soapdenovo2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers soapdenovo2
SOAPdenovo-127mer all -s config_file -K 63 -R -o graph_prefix 1>ass.log 2>ass.err