.. _backbone-label:

Khmer
==============================

Introduction
~~~~~~~~
Khmer is a tool for k-mer counting, filtering, and graph traversal FTW!


| For more information, please check:
| BioContainers: https://biocontainers.pro/tools/khmer 
| Home page: https://github.com/dib-lab/khmer

.. 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
    - 3.0.0a3
  * - BELL
    - 3.0.0a3
  * - GAUTSCHI
    - 3.0.0a3
  * - NEGISHI
    - 3.0.0a3
  * - SCHOLAR
    - 3.0.0a3

Commands
~~~~~~~
- abundance-dist.py
- abundance-dist-single.py
- annotate-partitions.py
- count-median.py
- cygdb
- cython
- cythonize
- do-partition.py
- extract-long-sequences.py
- extract-paired-reads.py
- extract-partitions.py
- fastq-to-fasta.py
- filter-abund.py
- filter-abund-single.py
- filter-stoptags.py
- find-knots.py
- interleave-reads.py
- load-graph.py
- load-into-counting.py
- make-initial-stoptags.py
- merge-partitions.py
- normalize-by-median.py
- partition-graph.py
- readstats.py
- sample-reads-randomly.py
- screed
- split-paired-reads.py
- trim-low-abund.py
- unique-kmers.py

Module
~~~~~~~~
You can load the modules by::

    module load biocontainers
    module load khmer

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 khmer 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=khmer
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers khmer

        # Your khmer 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=khmer
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers khmer

        # Your khmer 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=khmer
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers khmer

        # Your khmer 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=khmer
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers khmer

        # Your khmer 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=khmer
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers khmer

        # Your khmer workflow...