I’m excited to share our new preprint introducing HipHap, a tool for assigning long reads to haplotype-resolved diploid reference assemblies!

With Max Marin, Matthew Meyerson, and @lh3lh3.bsky.social

Preprint: www.biorxiv.org/content/10.6...
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Single-page, interactive overlap assembler for teaching purposes: lh3.github.io/teach-demo/o... (vibe coded)

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357