ish is a CLI tool for searching records using alignment methods. It’s record-type aware and supports lines, FASTA, and FASTQ. I was really pleased with the dev experience using Mojo. It’s still pre-1.0 and missing a few things, but overall it came together smoothly. Performance-wise, Mojo held up well. There's no direct apples-to-apples comparison for ish as a whole, but the core alignment algorithms are on par with the C++ reference (faster in one case, see preprint linked above). Writing and shipping a GPU kernel as part of a CLI was especially cool. This was my first time with GPU programming, and Mojo made it feel first-class, though I don't have much CUDA experience to compare. Excited to see where Mojo goes. Once the compiler is open-sourced, the possibilities look wide open.
Preprint can be found here: https://www.biorxiv.org/content/10.1101/2025.06.04.657890v1
Code can be found here: https://github.com/BioRadOpenSource/ish
