Thread by @rrwick

I've just released (during #MicroSeq2021) a new short-read polishing tool for fixing errors in long-read bacterial genome assemblies: Polypolish!
github.com/rrwick/Polypol…
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There are many other short-read polishing tools, including HyPo, NextPolish, ntEdit, Pilon and POLCA. So what does Polypolish do differently to warrant another?
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Most other polishers use 'normal' short-read alignments, where each read is aligned to one best location (randomly chosen in a tie). This works fine in non-repeat sequences, but errors in repeats often lead to a lack of alignments and therefore can't be fixed.
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Polypolish is instead designed to take alignments where each read is aligned to all possible locations, which ensures good coverage in repeats. So Polypolish can often fix errors in repeats that other polishers cannot.
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Here are some preliminary results from an in-progress paper. Each dot is a long-read bacterial genome assembly. Polypolish did well, but the best results came from using Polypolish in combination with other short-read polishers.
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Lots more information about how it works can be found on the Polypolish wiki:
github.com/rrwick/Polypol…
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Also, Polypolish was the first tool I've written in @rustlang. I'm still new to the language, but I like it a lot so far. Hopefully more Rust in my future!
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Thanks to @DrKatHolt, everyone in the Holt lab, the organisers of #MicroSeq2021 and all the other developers out there working on genome assembly and polishing 😄
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