Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

• Version: 0.3.2pre
• Added: February, 2020
• Updated: February, 2023
• Link: https://github.com/artic-network/Porechop

Note: the original repository was rrwick/Porechop but it was discontinued. The project was forked and continued by artic-network.

See which versions are available:

$ module avail porechop

Load one version into your environment and run it:

$ module load porechop/0.3.2pre
$ porechop

Notes from the sysadmin during installation:

$ git clone https://github.com/artic-network/Porechop.git -b v0.3.2pre
$ sudo mkdir -p /export/apps/porechop/0.3.2pre
$ sudo chown aorth /export/apps/porechop/0.3.2pre
$ module load python/3.8
$ python -m venv /export/apps/porechop/0.3.2pre
$ source /export/apps/porechop/0.3.2pre/bin/activate
$ pip install --upgrade setuptools pip wheel
$ source /export/apps/porechop/0.3.2pre/bin/activate
$ python setup.py install
$ sudo chown -R root:root /export/apps/porechop/0.3.2pre