allpathslg
Link to section 'Introduction' of 'allpathslg' Introduction
Allpathslg is a whole-genome shotgun assembler that can generate high-quality genome assemblies using short reads.
For more information, please check its website: https://biocontainers.pro/tools/allpathslg and its home page: https://bioinformaticshome.com/tools/wga/descriptions/Allpaths-LG.html.
Link to section 'Versions' of 'allpathslg' Versions
- 52488
Link to section 'Commands' of 'allpathslg' Commands
- PrepareAllPathsInputs.pl
- RunAllPathsLG
- CacheLibs.pl
- Fasta2Fastb
Link to section 'Module' of 'allpathslg' Module
You can load the modules by:
module load biocontainers
module load allpathslg
Link to section 'Example job' of 'allpathslg' 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 Allpathslg on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=allpathslg
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers allpathslg
PrepareAllPathsInputs.pl \
DATA_DIR=data \
PLOIDY=1 \
IN_GROUPS_CSV=in_groups.csv\
IN_LIBS_CSV=in_libs.csv\
OVERWRITE=True\
RunAllPathsLG PRE=allpathlg REFERENCE_NAME=test.genome \
DATA_SUBDIR=data RUN=myrun TARGETS=standard \
SUBDIR=test OVERWRITE=True