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.
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
to your script before loading a module. Then, you can list all versions of porechop-0.2.4 and load default version of porechop-0.2.4 as
module avail porechop-0.2.4/ # list available modules module load porechop-0.2.4 # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail porechop-0.2.4
and choose explicit version you want to use.
# Show help dialog of the 'Porechop' executable porechop-runner.py --help