ILRI Research Computing

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====== 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 =====

  * Version: 0.3.2pre
  * Added: February, 2020
  * Updated: February, 2023
  * Link: https://github.com/artic-network/Porechop

//Note:// the original repository was [[https://github.com/rrwick/Porechop|rrwick/Porechop]] but it was discontinued. The project was forked and continued by artic-network.

===== Usage =====

See which versions are available:
<code>$ module avail porechop</code>

Load one version into your environment and run it:
<code>$ module load porechop/0.3.2pre
$ porechop</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ 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</code>