Purge_dups

Introduction

purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/purge_dups
Home page: https://github.com/dfguan/purge_dups

Versions

  • 1.2.6

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

Module

You can load the modules by:

module load biocontainers
module load purge_dups

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 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