Ragnar {Groot Koerkamp} 🦋

PhD on high troughput bioinformatics @ ETH Zurich;
IMO, ICPC, Xoogler, Rust, road-cycling, hiking, wild camping, photography

[Mohammed Mudasser @Md_mudasser]

Key takeaways from @curious_coding session at #P99CONF :

🔹 Memory access bottlenecks priority queues.
🔹 SIMD-friendly layouts beat traditional heaps.
🔹 SimdQuickHeap is up to 2× faster than radix heaps.

Data layout matters! ⚡

@P99CONF @ScyllaDB #ScyllaDB

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

Live now!

[P99CONF @P99CONF]

Binary heaps are cache-inefficient and cause a cache miss on nearly every pop. In 20 minutes, @curious_coding dives into SimdQuickHeap and how it results in a priority queue that is up to 10x faster than binary and d-ary heaps. https://t.co/tVBWM2b0ub

#ScyllaDB #P99CONF

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

Thursday, 6:10pm CEST!

[ScyllaDB @ScyllaDB]

Our @P99CONF keynotes feature top engineers and system architects like @DorLaor, @curious_coding, @georg_kreuzmayr, and @reconditerose. At our free & virtual #P99CONF, you also get to interact with each of them. Join our October 21-22 event > https://t.co/GHPIyQBurl

#ScyllaDB

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

I'll be speaking at P99 later this month!

[ScyllaDB @ScyllaDB]

The SimdQuickHeap recursively partitions the data until the smallest element is found, and stores the pivots and buckets between them. @curious_coding will show how this is the fastest priority queue at our free @P99CONF on Oct. 21-22. https://t.co/oOae7JVuR6

#ScyllaDB #P99CONF

[Rust for Bioinformatics @rust4bio]

SIMD + Rust + pattern matching = Sassy, a small, sharp tool from @curious_coding et al., for fast sequence search. Proof that you don't need a giant framework to move the needle, sometimes you just need really well-written low-level code. 🔍🦀
https://t.co/J3kXTH9KEk

[antisense. @razoralign]

Sassy: Fuzzy Searching DNA Sequences using SIMD https://t.co/S91i43a2Yh

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

@jpelbers @heufd4 (feel free to make a gh issue with some more context)

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

To all folks dealing with biological data:
do you ever need to check if your reads contain barcodes/adapters/primers/...? Or off-target matches?

Sassy is the tool to use! A super fast implementation of "approximate string matching" with a grep-like CLI.

https://t.co/WWdcuh82Fb

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

@jpelbers @heufd4 Rick made Barbell for demultiplexing+trimming. I'm not actually sure if it supports just trimming though.

It might make sense to add this to sassy directly.
The hard part is choosing all the thresholds usually (# errors; dist to end; overhang cost).

https://t.co/Hn8D8tIHX7

[Samuel Lampa - Also: smllmp.bsky.social @smllmp]

As said before, this is a super useful (and *fast*) tool, that we've already been using quite a bit for troubleshooting spurious primer matching and the like. Warmly recommended!

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

@heufd4 ❤️

Basically "fuzzy grep for fasta files": search fasta/fastq files for short DNA patterns to verify that they are present/absent in the data in the right places, and what kind of errors there are.

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

https://t.co/9XwyNVhpIs

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

New preprint!
The SimdQuickHeap is the fastest priority queue, by far.
2x faster than a radix heap, and up to 10x faster than binary heaps.

Coauthored with Johannes Breitling and Marvin Williams.

[Data Structures and Algorithms Papers @AlgorithmPapers]

SimdQuickHeap: The QuickHeap Reconsidered

Johannes Breitling, Ragnar Groot Koerkamp, Marvin Williams
https://t.co/FMY7iqpEce [𝚌𝚜.𝙳𝚂]

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

As often: the SimdQuickHeap is a conceptually very simple data structure that thus can be easily optimized using SIMD, leading to pretty big speed gains.

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

https://t.co/ftWJFOqxEa

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

New preprint!
The SimdQuickHeap is the fastest priority queue, by far.
2x faster than a radix heap, and up to 10x faster than binary heaps.

Coauthored with Johannes Breitling and Marvin Williams.

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

OMG! By popular demand (🤗) I'm going to speak at P99 again!
This time about the SimdQuickHeap preprint that just came out: the fastest priority queue by 2x (or 10x comparing to a binary heap).

[P99CONF @P99CONF]

We've been working hard behind the scenes to bring you an unforgettable P99CONF 2026. Registration is now open, so take a look at who is coming back and the new speakers we have on board > https://t.co/HMlcvQNjFs

#ScyllaDB #P99CONF

[Data Structures and Algorithms Papers @AlgorithmPapers]

SimdQuickHeap: The QuickHeap Reconsidered

Johannes Breitling, Ragnar Groot Koerkamp, Marvin Williams
https://t.co/FMY7iqpEce [𝚌𝚜.𝙳𝚂]