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.

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

See which versions are available:

$ module avail polypolish

Load one version into your environment and run it:

$ module load polypolish/0.6.0
$ polypolish

Notes from the sysadmin during installation:

$ 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