purge_dups
Link to section 'Introduction' of 'purge_dups' Introduction
purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.
BioContainers: https://biocontainers.pro/tools/purge_dups
Home page: https://github.com/dfguan/purge_dups
Link to section 'Versions' of 'purge_dups' Versions
- 1.2.6
Link to section 'Commands' of 'purge_dups' Commands
- augustify.py
- bamToWig.py
- cleanup-blastdb-volumes.py
- edirect.py
- executeTestCGP.py
- extractAnno.py
- findRepetitiveProtSeqs.py
- fix_in_frame_stop_codon_genes.py
- generate_plot.py
- getAnnoFastaFromJoingenes.py
- hist_plot.py
- pd_config.py
- run_abundance.py
- run_purge_dups.py
- run_sepp.py
- run_tipp.py
- run_tipp_tool.py
- run_upp.py
- split_sequences.py
- stringtie2fa.py
- sumlabels.py
- sumtrees.py
Link to section 'Module' of 'purge_dups' Module
You can load the modules by:
module load biocontainers
module load purge_dups
Link to section 'Example job' of 'purge_dups' 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 purge_dups on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=purge_dups
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers purge_dups