Rewrites.bio: 60x speedup in Genomics QC and AI rewrite principles for Science

AI coding assistants have made it possible for domain experts to rewrite established scientific software in days. We believe that a wave of AI-driven tool rewrites is coming to bioinformatics. We've published a set of best-practices principles to help people to approach rewrites in the right way. Along the way we fully rewrote and open-sourced the genomics QC tools for RNAseq, the most widely used genomics pipeline, yielding a >60x performance improvement.

So needed. I just threw genebody_coverage and TIN out of RSeQC ;) Maybe they can come back now.

Really interesting direction. The validation and drop-in compatibility part is what caught my attention most. If this holds up across more datasets, this could remove a huge amount of RNA-seq QC runtime pain.