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replacing FastANI with skani for faster computations for the cluster command #155

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jianshu93 opened this issue Jan 21, 2023 · 0 comments

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@jianshu93
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Hello Ben,

This is Jianshu again, recently our team here at Georgia tech review a very interesting paper (https://www.biorxiv.org/content/10.1101/2023.01.18.524587v1), the tool is called skani, which further accelerate FastANI by 20 times via even faster seeding and chaining technique and also FracMinHash (https://www.biorxiv.org/content/10.1101/2022.01.11.475870v3.abstract). More importantly it is fully parallelized and written in Rust. I tried and benchmarked it against blast based ani an also orthoANI (as in the paper) and it is just as good as FastANI while being 20X faster. I believe integrating it into coverm cluster will be very easy since the code is very clear to me.

Thanks,

Jianshu

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