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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).
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. 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.