.. _backbone-label:

Seqcode
==============================

Introduction
~~~~~~~~
SeqCode is a family of applications designed to develop high-quality images and perform genome-wide calculations from high-throughput sequencing experiments. This software is presented into two distinct modes: web tools and command line. The website of SeqCode offers most functions to users with no previous expertise in bioinformatics, including operations on a selection of published ChIP-seq samples and applications to generate multiple classes of graphics from data files of the user. On the contrary, the standalone version of SeqCode allows bioinformaticians to run each command on any type of sequencing data locally in their computer. The architecture of the source code is modular and the input/output interface of the commands is suitable to be integrated into existing pipelines of genome analysis. SeqCode has been written in ANSI C, which favors the compatibility in every UNIX platform and grants a high performance and speed when analyzing sequencing data. Meta-plots, heatmaps, boxplots and the rest of images produced by SeqCode are internally generated using R. SeqCode relies on the RefSeq reference annotations and is able to deal with the genome and assembly release of every organism that is available from this consortium.


| For more information, please check:
| Docker hub: https://hub.docker.com/r/eblancocrg/seqcode 
| Home page: https://github.com/eblancoga/seqcode

.. 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
    - 1.0
  * - BELL
    - 1.0
  * - GAUTSCHI
    - 1.0
  * - NEGISHI
    - 1.0
  * - SCHOLAR
    - 1.0

Commands
~~~~~~~
- buildChIPprofile
- combineChIPprofiles
- combineTSSmaps
- combineTSSplots
- computemaxsignal
- findPeaks
- genomeDistribution
- matchpeaks
- matchpeaksgenes
- processmacs
- produceGENEmaps
- produceGENEplots
- producePEAKmaps
- producePEAKplots
- produceTESmaps
- produceTESplots
- produceTSSmaps
- produceTSSplots
- recoverChIPlevels
- scorePhastCons

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

    module load biocontainers
    module load seqcode

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

        module --force purge
        module biocontainers seqcode

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

        module --force purge
        module biocontainers seqcode

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

        module --force purge
        module biocontainers seqcode

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

        module --force purge
        module biocontainers seqcode

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

        module --force purge
        module biocontainers seqcode

        # Your seqcode workflow...