.. _backbone-label:

Lyveset
==============================

Introduction
~~~~~~~~
Lyveset is a method of using hqSNPs to create a phylogeny, especially for outbreak investigations.


| For more information, please check:
| Docker hub: https://hub.docker.com/r/staphb/lyveset 
| Home page: https://github.com/lskatz/lyve-SET

.. 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
    - 2.0.1
  * - BELL
    - 2.0.1
  * - GAUTSCHI
    - 2.0.1
  * - NEGISHI
    - 2.0.1
  * - SCHOLAR
    - 2.0.1

Commands
~~~~~~~
- applyFstToTree.pl
- cladeDistancesFromTree.pl
- clusterPairwise.pl
- convertAlignment.pl
- downloadDataset.pl
- errorProneRegions.pl
- filterMatrix.pl
- filterVcf.pl
- genomeDist.pl
- launch_bwa.pl
- launch_set.pl
- launch_smalt.pl
- launch_snap.pl
- launch_snpeff.pl
- launch_varscan.pl
- makeRegions.pl
- matrixToAlignment.pl
- pairwiseDistances.pl
- pairwiseTo2d.pl
- removeUninformativeSites.pl
- removeUninformativeSitesFromMatrix.pl
- run_assembly_isFastqPE.pl
- run_assembly_metrics.pl
- run_assembly_readMetrics.pl
- run_assembly_removeDuplicateReads.pl
- run_assembly_shuffleReads.pl
- run_assembly_trimClean.pl
- set_bayesHammer.pl
- set_diagnose.pl
- set_diagnose_msa.pl
- set_downloadTestData.pl
- set_findCliffs.pl
- set_findPhages.pl
- set_indexCase.pl
- set_manage.pl
- set_processPooledVcf.pl
- set_samtools_depth.pl
- set_test.pl
- shuffleSplitReads.pl
- snpDistribution.pl
- vcfToAlignment.pl
- vcfutils.pl

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

    module load biocontainers
    module load lyveset

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

        module --force purge
        module biocontainers lyveset

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

        module --force purge
        module biocontainers lyveset

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

        module --force purge
        module biocontainers lyveset

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

        module --force purge
        module biocontainers lyveset

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

        module --force purge
        module biocontainers lyveset

        # Your lyveset workflow...