we also have a Rust implementation of the core engine, but it’s there because we want a native library without dependencies and good UTF-8 support, not because it’s necessarily faster. in fact, the F# version is faster than the Rust version - .NET has an effortless way to vectorize regexes with SearchValues<T, and our implementation is able to detect and utilize these opportunities when most other engines can’t. replicating what .NET gives you for free would take considerable effort, and i haven’t done that in Rust yet - especially since many existing SIMD subroutines only work left to right, while .NET also provides right-to-left variants needed for our bidirectional matching.
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Detecting fluorescence from a single DNA molecule proved difficult in practice, however. And so, in 2004, Solexa acquired the IP rights to a method called colony sequencing, developed by French scientists Pascal Mayer and Laurent Farinelli, to solve the detection problem. Colony sequencing affixed DNA fragments to a surface and amplified them over and over, generating “colonies” containing massive numbers of identical DNA strands. By reading the fluorescence from each strand in a colony simultaneously, it became possible to determine the base added at each step with much better accuracy, since random errors in individual strands would be averaged out by the consensus signal.