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

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	1.2.6_fixed, 1.2.6
BELL	1.2.6_fixed, 1.2.6
GAUTSCHI	1.2.6
NEGISHI	1.2.6_fixed, 1.2.6
SCHOLAR	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:

Anvil

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition 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
module biocontainers purge_dups

# Your purge_dups workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers purge_dups

# Your purge_dups workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers purge_dups

# Your purge_dups workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers purge_dups

# Your purge_dups workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers purge_dups

# Your purge_dups workflow...