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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/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.

cutadapt-software.txt · Last modified: 2021/12/15 07:33 by aorth