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Fasten v0.9.10 just released! Memory allocation was updated, resulting in a massive speed up. The benchmark can be found here: github.com/lskatz/faste...

github.comDouble pointer indirection in src/io/seq.rs · Issue #47 · lskatz/fastenHi, the Clearable trait methods in src/io/seq.rs takes &String arguments. This leads to two layers of indirection: dereferencing &String to jump to the String which itself contains the address and ...

Lee Katz

@lskatz.github.io

8 Sept

Here is the original read cleaning speed vs the new read cleaning speed. As compared to seqtk, fasten now performs in the same magnitude.

Lee Katz

@lskatz.github.io

8 Sept

Kmer counting is another massive speedup. Original vs new. Fasten actually performs faster than Jellyfish.

Lee Katz

@lskatz.github.io

8 Sept

Fasten got much faster at regular expressions. Check out this comparison from before vs now

Lee Katz

@lskatz.github.io

8 Sept

I'll do one more. Fasten is now just about as fast as trusted unix utilities for sorting sequences. Original vs new version of Fasten.

Lee Katz

@lskatz.github.io

Anyway, check out the newest version of Fasten v0.9.10! No algorithmic differences, but yes a massive speedup!

8/9/26, 2:43 am0 reposts1 like

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