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Rick Beeloo

@rickbitloo.bsky.social

PhD candidate Utrecht University Some bio and coding stuff

18 Posts79 Follower38 Folgt
Ragnar {Groot Koerkamp}@curiouscoding.nl · 5mo ago

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!

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 5mo ago

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

Ragnar {Groot Koerkamp}@curiouscoding.nl · 9mo ago

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.
Ragnar {Groot Koerkamp}@curiouscoding.nl · 10mo ago

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.

Rick Beeloo@rickbitloo.bsky.social · 10mo ago

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...