====== polypolish ======

Polypolish is a tool for polishing genome assemblies with short reads. Unlike other polishers, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Polypolish is also a conservative polisher, so it is very unlikely to introduce new errors during polishing.

===== Information =====

  * Version: 0.6.0
  * Added: May, 2025
  * Link: https://github.com/rrwick/Polypolish

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load polypolish/0.6.0
$ polypolish</code>

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

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget https://github.com/rrwick/Polypolish/releases/download/v0.6.0/polypolish-linux-x86_64-musl-v0.6.0.tar.gz
$ sudo mkdir -p /export/apps/polypolish/0.6.0/bin
$ sudo tar xf polypolish-linux-x86_64-musl-v0.6.0.tar.gz -C /export/apps/polypolish/0.6.0/bin</code>