Antoine Limasset
npmalfoy.bsky.social
CNRS researcher in bioinformatics Lille, France (Bonsai team). I develop efficient computational methods to analyze massive sequencing data, creating scalable tools for genomics, transcriptomics, and metagenomics. https://malfoy.github.io/
👤 Joined on 02 janvier 2025
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- 02 Oca 2025, 10:11
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Already used in packed_seq when reading a fastx file into a single bit-packed vector. The multithreading when reading uncompressed fasta files allows for something like 20GB/s!
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bowtie2 just got 37X faster in the browser! Using WebAssembly SIMD, aligning 1M reads went from 19min to 30s, close to native speeds. It's now practical to run sequence alignment in the browser. Available on biowasm today: biowasm.com/cdn/v3/bowti... cc @benlangmead.bsky.social
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In all our latest software at Bonsai 🤩
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Glad to announce a big new release of Helicase, my Rust library for FASTA/Q parsing and bitpacking! With this new version, it's now consistently the fastest Rust parser (1.1-4x faster than needletail) and supports parallel processing!
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If humans don't write the proofs anymore, why not put the x86 instruction set into the model, and the cache hierarchy, pipelining details, scheduling, multithreading, everything! We could have actual predicted wall-clock running times on actual machines. Wouldn't that be amazing?
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