Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
See available versions of cutadapt:
$ module avail cutadapt
Load one version into your environment and run it:
$ module load cutadapt/1.18 $ cutadapt
Notes from the sysadmin during installation:
$ 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
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.