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soapdenovo2.rst

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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 and its home page: http://soap.genomics.org.cn/soapdenovo.html.

Versions

  • 2.40

Commands ~~~~~~~ - SOAPdenovo-127mer - SOAPdenovo-63mer

Module

You can load the modules by:

module load biocontainers
module load soapdenovo2

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 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