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cutadapt-software

cutadapt

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

Information

Usage

See available versions of cutadapt:

$ module avail cutadapt

Load one version into your environment and run it:

$ module load cutadapt/1.18
$ cutadapt

Installation

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.

cutadapt-software.txt · Last modified: 2019/01/20 13:45 by aorth