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
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.