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Software requirements
Ryan Wick edited this page Jul 23, 2021
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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 prebuilt 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.
Other short-read aligners like Bowtie 2 and minimap2 may work with Polypolish, but I haven't tested them myself.