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.
See which versions of porechop are available:
$ module avail porechop
Load one version into your environment and run it:
$ module load porechop/0.2.4 $ porechop
Notes from the sysadmin during installation:
$ git clone https://github.com/rrwick/Porechop.git -b v0.2.4 $ cd Porechop $ sudo mkdir -p /export/apps/porechop/0.2.4 $ sudo chown aorth /export/apps/porechop/0.2.4 $ python3 -m venv /export/apps/porechop/0.2.4 $ source /export/apps/porechop/0.2.4/bin/activate $ scl enable devtoolset-7 bash $ python3 setup.py install $ sudo chown -R root:root /export/apps/porechop/0.2.4