cutadapt

cutadapt is a software module available on Comet.

To access cutadapt on Comet, run module load cutadapt. This will load the default version of cutadapt.

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

cutadapt:
     Versions:
        cutadapt/4.9-GCCcore-12.3.0
        cutadapt/4.9 (E)

Names marked by a trailing (E) are extensions provided by another module.

  For detailed information about a specific "cutadapt" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider cutadapt/4.9

If there are multiple versions of cutadapt listed, then you can load a specific version as follows:

$ module load cutadapt/version_string

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

The module cutadapt has the following embedded help text (module help cutadapt):

Description
===========
Cutadapt finds and removes adapter sequences, primers, poly-A tails and
 other types of unwanted sequence from your high-throughput sequencing reads.

More information
================
 - Homepage: https://opensource.scilifelab.se/projects/cutadapt/

Included extensions
===================
cutadapt-4.9, dnaio-1.2.1, xopen-1.7.0

The default version of the module cutadapt has the following dependencies:

• GCCcore/12.3.0
• pigz/2.8-GCCcore-12.3.0
• Python/3.11.3-GCCcore-12.3.0
• python-isal/1.1.0-GCCcore-12.3.0

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