Purdue University

Commands

• RepeatScout
• build_lmer_table
• compare-out-to-gff.prl
• filter-stage-1.prl
• filter-stage-2.prl
• merge-lmer-tables.prl

Module

You can load the modules by:

module load biocontainers
module load repeatscout

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 RepeatScout on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=repeatscout
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers repeatscout

build_lmer_table -l 14 -sequence genome.fasta -freq Final_assembly.freq

RepeatScout -sequence genome.fasta -output Final_assembly_repeats.fasta -freq Final_assembly.freq -l 14