ILRI Research Computing

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

===== Information =====

  * Version: 3.5
  * Added: June, 2015
  * Updated: December, 2021
  * Link: https://github.com/marcelm/cutadapt

===== Usage =====

See available versions of cutadapt:
<code>$ module avail cutadapt</code>

Load one version into your environment and run it:
<code>$ module load cutadapt/3.5
$ cutadapt</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ sudo mkdir -p /export/apps/cutadapt/3.5
$ sudo chown aorth /export/apps/cutadapt/3.5
$ python3 -m venv /export/apps/cutadapt/3.5
$ source /export/apps/cutadapt/3.5/bin/activate
$ pip install --upgrade setuptools pip
$ pip install cutadapt==3.5
$ sudo chown -R root:root /export/apps/cutadapt/3.5</code>

Installation is greatly simplified by using Python 3's built-in venv module to create a dedicated environment, then use standard pip to install cutadapt and its dependencies.