Sassy2: Batch Searching of Short DNA Patterns https://www.biorxiv.org/content/10.64898/2026.03.10.710811v1

It's a good day when the first item in your feed is your own work :) @rickbitloo.bsky.social was annoyed that scanning reads for all 96 rapid kit barcodes is bottleneck in Barbell, so he made Sassy2: 13x (150bp) to 4.6x (8kbp) faster than v1 by batch-searching patterns, and >100Gbp/s on 16 threads!

If you ever need to fuzzy search some DNA, sassy is your tool. Please spread the word; I think many people just outside my own circle could benefit from this :) cc @rickbitloo.bsky.social github.com/RagnarGrootK...

Following ish's `filter` and bqtools' `grep`, Sassy now also has initial support for grep and filter! Grep mode shows all matches, grouped per record, and is meant for human consumption. Filter mode prints full matching (or non-matching) records to stdout or output files.

Really exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.

Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data https://www.biorxiv.org/content/10.1101/2025.10.22.683865v1

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

Now also on biorxiv :)

Sassy is out now! Ever need to search for approximate matches of short DNA strings? Sassy is the tool to use! Available now wherever you get your code With @rickbitloo.bsky.social curiouscoding.nl/papers/sassy... github.com/ragnarGrootK...