Software requirements

Polypolish runs on macOS and Linux. It is coded in Rust, so you'll need to install Rust if you want to build Polypolish from source. However, many users can simply download pre-built binaries for their OS and will therefore not need Rust installed (see Installation for more detail).

Aligner

Polypolish takes SAM files from the BWA-MEM aligner as input, so you will want to have that tool installed. Alternatively, you can use minibwa which is the successor to BWA-MEM. Bowtie 2 should also work, though I've tested it less. Other short-read aligners like minimap2 may work with Polypolish, but I haven't tested them myself. Read more about alternative aligners on the FAQ and miscellaneous tips page.