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

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

See available versions of cutadapt:

$ module avail cutadapt

Load one version into your environment and run it:

$ module load cutadapt/3.5
$ cutadapt

Notes from the sysadmin during installation:

$ 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

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.