====== 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: 1.18
  * Added: June, 2015
  * Updated: January, 2019
  * 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/1.18
$ cutadapt</code>

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

<code>$ sudo mkdir -p /export/apps/cutadapt/1.18
$ sudo chown aorth /export/apps/cutadapt/1.18
$ python36 -m venv /export/apps/cutadapt/1.18
$ . /export/apps/cutadapt/1.18/bin/activate
$ pip install --upgrade pip setuptools
$ pip install cutadapt==v1.18
$ sudo chown -R root:root /export/apps/cutadapt/1.18</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.