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
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