User Tools

Site Tools



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 -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 install
$ sudo chown -R root:root /export/apps/porechop/0.2.4
porechop-software.txt · Last modified: 2020/02/27 11:12 by aorth