User Tools

Site Tools


porechop-software

porechop

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.

Information

Usage

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

Installation

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
porechop-software.txt · Last modified: 2020/02/27 11:12 by aorth