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Rick Beeloo

@rickbitloo.bsky.social

80 followers 38 following 18 posts

PhD candidate Utrecht University Some bio and coding stuff

Posts Replies Media

Reposted by Rick Beeloo

Ragnar {Groot Koerkamp} @curiouscoding.nl · 26/05/2026

Turns out I presented Sassy yesterday without realising it has been published! Finally officially a coauthor with @rickbitloo.bsky.social 😆 doi.org/10.1093/bioi...

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Reposted by Rick Beeloo

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 12/03/2026

Sassy2: Batch Searching of Short DNA Patterns www.biorxiv.org/content/10.64898/20…

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Reposted by Rick Beeloo

Ragnar {Groot Koerkamp} @curiouscoding.nl · 13/03/2026

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!

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Reposted by Rick Beeloo

Ragnar {Groot Koerkamp} @curiouscoding.nl · 10/12/2025

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...

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Reposted by Rick Beeloo

Ragnar {Groot Koerkamp} @curiouscoding.nl · 30/10/2025

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.

Output of `sassy grep -p ACTGGCATGAGAACTGAG -k1 human-genome.fa`. Should fuzzy matches with up to one error, grouped by file, then by record. The matching part is highlighted with colours (green=match, orange=mismatch, red=delete, blue=insert), and the strandedness of each match, the location, and the cost are shown.

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Reposted by Rick Beeloo

Ragnar {Groot Koerkamp} @curiouscoding.nl · 23/10/2025

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.

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Reposted by Rick Beeloo

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 23/10/2025

Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data www.biorxiv.org/content/10.1101/202…

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Rick Beeloo @rickbitloo.bsky.social · 23/10/2025

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...

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Reposted by Rick Beeloo

Ragnar {Groot Koerkamp} @curiouscoding.nl · 26/07/2025

Now also on biorxiv :)

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Reposted by Rick Beeloo

Ragnar {Groot Koerkamp} @curiouscoding.nl · 18/07/2025

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...

Sassy solves approximate string matching: finding all matches of a pattern in a text.

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