.. _backbone-label:

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
~~~~~~~
.. list-table::
  :width: 100 %
  :widths: 25 75
  :header-rows: 1

  * - 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:

.. tab-set::

  .. tab-item:: Anvil

    .. code-block:: bash

        #!/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...

  .. tab-item:: Bell, Gautschi, or Negishi

    .. code-block:: bash

        #!/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...

  .. tab-item:: Gautschi-AI

    .. code-block:: bash

        #!/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...

  .. tab-item:: Gilbreth

    .. code-block:: bash

        #!/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...

  .. tab-item:: Scholar

    .. code-block:: bash

        #!/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...