.. _backbone-label:

Idba
==============================

Introduction
~~~~~~~~
Idba is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.


| For more information, please check:
| BioContainers: https://biocontainers.pro/tools/idba 
| Home page: https://i.cs.hku.hk/~alse/hkubrg/projects/idba/index.html

.. 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
    - 1.1.3
  * - BELL
    - 1.1.3
  * - GAUTSCHI
    - 1.1.3
  * - NEGISHI
    - 1.1.3
  * - SCHOLAR
    - 1.1.3

Commands
~~~~~~~
- fa2fq
- filter_blat
- filter_contigs
- filterfa
- fq2fa
- idba
- idba_hybrid
- idba_tran
- idba_tran_test
- idba_ud
- parallel_blat
- parallel_rna_blat
- print_graph
- raw_n50
- run-unittest.py
- sample_reads
- scaffold
- scan.py
- shuffle_reads
- sim_reads
- sim_reads_tran
- sort_psl
- sort_reads
- split_fa
- split_fq
- split_scaffold
- test
- validate_blat
- validate_blat_parallel
- validate_component
- validate_contigs_blat
- validate_contigs_mummer
- validate_reads_blat
- validate_rna

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

    module load biocontainers
    module load idba

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

        module --force purge
        module biocontainers idba

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

        module --force purge
        module biocontainers idba

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

        module --force purge
        module biocontainers idba

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

        module --force purge
        module biocontainers idba

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

        module --force purge
        module biocontainers idba

        # Your idba workflow...