====== Trim_Galore ======

**Trim_Galore** is a software module available on **Comet**.

===== Trim_Galore overview =====

To access **Trim_Galore** on Comet, run ''module load Trim_Galore''. This will load the //default// version of **Trim_Galore**.

An overview of the module information is shown below (''module -r spider ^Trim_Galore$''):

<code lang=text>
  Trim_Galore: Trim_Galore/0.6.10-GCCcore-12.3.0
    Description:
      Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality
      to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).

    This module can be loaded directly: module load Trim_Galore/0.6.10-GCCcore-12.3.0

    Help:
      
      Description
      ===========
      Trim Galore! is a wrapper script to automate quality and adapter
      trimming as well as quality control, with some added functionality to remove biased
      methylation positions for RRBS sequence files (for directional, non-directional
      (or paired-end) sequencing).
      
      More information
      ================
       - Homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
</code>

If there are multiple versions of **Trim_Galore** listed, then you can load a //specific// version as follows:
<code lang=bash>
$ module load Trim_Galore/version_string
</code>

You can find the most //up to date information// whilst logged on to Comet by running ''module -r spider ^Trim_Galore$''.

----

===== Trim_Galore Help =====

The module **Trim_Galore** has the following embedded help text (''module help Trim_Galore''):

<code lang=text>Description
===========
Trim Galore! is a wrapper script to automate quality and adapter
trimming as well as quality control, with some added functionality to remove biased
methylation positions for RRBS sequence files (for directional, non-directional
(or paired-end) sequencing).

More information
================
 - Homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

</code>

----

===== Trim_Galore Dependencies =====

The //default// version of the module **Trim_Galore** has the following dependencies:

   * GCCcore/12.3.0
   * Python/3.11.3-GCCcore-12.3.0
   * Java/11
   * pigz/2.8-GCCcore-12.3.0
   * Perl/5.36.1-GCCcore-12.3.0
   * cutadapt/4.9-GCCcore-12.3.0
   * FastQC/0.11.9-Java-11

----

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