-
Notifications
You must be signed in to change notification settings - Fork 10
Software requirements
Polypolish runs on macOS and Linux. It requires Python 3.6 or later. It doesn't require any Python packages (unless you want to run the automated tests in which case you'll need Pytest).
Since Polypolish is implemented entirely in Python, you can optionally install/run it with PyPy for better performance. I would therefore recommend that you install PyPy before installing Polypolish, if you can.
If you use PyPy, you'll need a version which supports Python 3.6 or later. Check this by running pypy3 --version.
Polypolish takes SAM files from the BWA aligner as input, so you will want to have that tool installed. It's easy to build from source (just clone, make and copy the single executable into your path), or else you can use a package manager such as Homebrew or APT.
Alternatively, you can use the Bwa-mem2 tool which is a faster implementation of BWA.
Other short-read aligners like Bowtie 2 and minimap2 may work with Polypolish, but I haven't tested this myself.