repeatscout
Link to section 'Introduction' of 'repeatscout' Introduction
RepeatScout is a tool to discover repetitive substrings in DNA.
For more information, please check its website: https://biocontainers.pro/tools/repeatscout and its home page on Github.
Link to section 'Versions' of 'repeatscout' Versions
- 1.0.6
Link to section 'Commands' of 'repeatscout' Commands
- RepeatScout
- build_lmer_table
- compare-out-to-gff.prl
- filter-stage-1.prl
- filter-stage-2.prl
- merge-lmer-tables.prl
Link to section 'Module' of 'repeatscout' Module
You can load the modules by:
module load biocontainers
module load repeatscout
Link to section 'Example job' of '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