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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.


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 -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 install
$ sudo chown -R root:root /export/apps/porechop/0.3.2pre
porechop-software.txt · Last modified: 2023/02/23 06:39 by aorth