@curious_coding

PhD on high troughput bioinformatics @ ETH Zurich; IMO, ICPC, Xoogler, Rust, road-cycling, hiking, wild camping, photography https://xitter.cf/t.co/wBv2zN4F80

 Zurich
curiouscoding.nl
Joined October 2021
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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. curiouscoding.nl/posts/sassy…
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With AVX-512, the SimdQuickHeap is consistently 2x faster than the radix heap and other engineered heaps that are I/O-efficient, and up to 10x faster than the binary heap and other tree-based heaps.
Log-log time-per-operation plots for different workloads. The x-ax has increasing input sizes, and the y-ax has the normalized time per push-pop pair of operations divided by lg n. The binary heap, d-ary heap, and weak heap all slow down as n increases, while the I/O-efficient heaps all get faster. The SimdQuickHeap is 2x faster than the radix heap and up to 10x faster than the binary heap.

ALT Log-log time-per-operation plots for different workloads. The x-ax has increasing input sizes, and the y-ax has the normalized time per push-pop pair of operations divided by lg n. The binary heap, d-ary heap, and weak heap all slow down as n increases, while the I/O-efficient heaps all get faster. The SimdQuickHeap is 2x faster than the radix heap and up to 10x faster than the binary heap.

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The data structure has some similarities to QuickSelect and is pretty simple: repeatedly partition the list of values using random pivots until the smallest is left, and store each part in its own array. New elements are compared to the pivots and pushed to the right layer.
Overview of the SimdQuickHeap data structure: a list (vector) of pivots is stored, and the elements between consecutive pivots are stored in their own bucket (also a vector). The elements in a bucket are in between the two pivots surrounding it.

ALT Overview of the SimdQuickHeap data structure: a list (vector) of pivots is stored, and the elements between consecutive pivots are stored in their own bucket (also a vector). The elements in a bucket are in between the two pivots surrounding it.

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Sassy, a tool for fast approximate string matching (eg searching short DNA strings) is out now! Conceptually simple but very nice work with Rick Beeloo.
bioRxiv Bioinfo@biorxiv_bioinfo26 Jul 2025
Sassy: Searching Short DNA Strings in the 2020s biorxiv.org/content/10.1101/… #biorxiv_bioinfo

Sassy: Searching Short DNA Strings in the 2020s

Motivation Approximate string matching (ASM) is the problem of finding all occurrences of a pattern P in a text T while allowing up to k errors. ASM was researched extensively around the 1990s, but...

biorxiv.org
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Meanwhile, the paper with @BKille , Todd, and others on a lower bound on the density of sampling/minimizer schemes was published! For k = 1 (mod w), the precise version (red) is the first to *exactly* match the density of optimal schemes found by ILP. doi.org/10.1093/bioinformati…
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Replying to @sasuke___420
OMG YES I CAN 😍 Definitely one to remember. I run into this semi-regularly, and never knew of a workaround before.
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New day, same old.
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I'm extra annoyed because the same happened last year for my 1BRC post and the video @theo made about it. I think around half of the 40 minute video is on my blog, yet it wasn't linked in the description either. youtube.com/watch?v=e_9ziFKc…
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Also, the BY part means a link must be shared. The link was not in the description when I was 4h into the stream, and live comments asked for it multiple times. Stream started between 2pm and 3pm CET, and from my server logs, I get the first referrals from YT at 17:17.
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Well great, watching live worked but now it's subscribers only. Not ideal😞 Also, my blog is CC-BY-SA, which _does_ allow others to make money off of it (since I get paid a salary anyway), as long as it's under the same licence. Private videos don't exactly feel share-alike? 🤔
Ragnar {Groot Koerkamp} 🦋@curious_coding6 Jan 2025
Prime is streaming my blog! Watch live now! (I'm out, will have to rewatch tonight lol) youtube.com/live/OSN-nkxGUXU…
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