Kristoffer Sahlin

DSB Program is out !
Seems incredible (as ever)
dsb-meeting.github.io/DSB2026/

recomb-seq.github.io/seq2026/keyd...

Multi-context seeds enable fast and high-accuracy read mapping A key step in sequence similarity search is to identify shared seeds between a query and a reference sequence. A well-known tradeoff is that longer seeds offer fast searches but reduce sensitivity in ...

... and the preprint has also been updated: www.biorxiv.org/content/10.1...

The commit benefited tremendously by minimap2’s practical algorithmic solutions for chaining and rescue -- big credits to @lh3lh3.bsky.social and his minimap2. Also to my students Nicolas Buchin and Ivan Tolstoganov, as well as Marcel Martin 4/4

Strobealign can now map long reads. Still POC, i.e., PAF only -- no supplementary chains or piecewise extension (yet). 3/4

Accuracy upgrades: chaining instead of NAMs, smarter local rescue of repetitive hits (minimap2-style), and improved multi-context seeding 2/4

Release Version 0.17.0 · ksahlin/strobealign Changes #504: Introduce collinear chaining as the new default mapping and alignment method, replacing NAMs. This reproduces the Minimap2 chaining algorithm providing better mapping accuracy. NAMs ...

Strobealign v0.17.0 is out! github.com/ksahlin/stro...

Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

Congratulations to Rayan Chiki, (Institut Pasteur) head of the “Sequence Bioinformatics” unit, for securing the ERC Proof of Concept 2025 for his project ENZYMINER! 👏

‪@rayan.chiki.bsky.social

#Bioinformatics

Incredible! 👏

We have officially started #HitSeq track @hitseq.bsky.social at #ISMBECCB2025. Francisco de la Vega, introduces our first #keynote speaker Valentina Boeva @valboeva.bsky.social with her talk: "Learning variant effects on chromatin accessibility and 3D structure without matched Hi-C data"

Meet our amazing sponsor PacBio @pacbio.bsky.social for @hitseq.bsky.social track at #ISMBECCB2025 represented by Elizabeth Tseng with her talk "Bioinformatics analysis for long-read RNA sequencing: challenges and promises" #hitseq #iscb #sequencing #application #iverpool #uk

Dont miss any of our #LongTREC communications at #ISMBECCB2025. Download this flyer to make catching all the latest & hottest long-read transcriptomics research simple.

@anaconesa.bsky.social

@hitseq.bsky.social is kicking off with our first keynote @valboeva.bsky.social talking about "Learning variant effects on chromatin accessibility and 3D structure without matched Hi-C data". #ISMBECCB2025

📽️ Next in the LongTREC Series: Mahmud Sami Aydin!
Sami is a Doctoral Candidate at @stockholm-uni.bsky.social , working under the supervision of @ksahlin.bsky.social .In this video, Sami shares his research and his role in the broader LongTREC collaboration across Europe.
#AlgorithmDevelopment

OReO: optimizing read order for practical compression AbstractMotivation. Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and mana

Paper alert!
We present Oreo a tools that reorder long reads datasets in a way to compress them efficiently with ANY universal compressor like gz, zstd, xz ...
TLDR: You can get state of the art compression WITHOUT a dedicated compressor/decompressor!
academic.oup.com/bioinformati...
A thread!

I worked with Thomas during a three months research visit during his PhD, and it resulted in a paper in NAR. I highly recommend him. doi.org/10.1093/nar/...

Thomas Baudeau defended his thesis on Studying the properties of viral long reads mapping methods - congrats docteur Baudeau you'll be deeply missed in the team. I'm very glad I got the chance to work with you. Thomas is also on the lookout for a postdoc 👀

🧵1/n
Estimating mutation rates using k-mers is fast—but what happens when repeats dominate the genome?

In a new preprint, Haonan Wu, Antonio Blanca, and myself propose a *repeat-aware* estimator that's accurate even in centromeres.

Hey yeast lovers. Do you like pangenomes?
O'Donnel et al. 2023 produced T2T assemblies of different strains, including phased haplotypes for yeast.

Here I selected 10 phased haplotypes and the S288C reference,
and looked for the MST28 / YAR033W gene reported to contain SVs such as indels.

👇🏻👇🏻

Congrats 👏👏

IMO it matters a lot as a 'first impression'

I did only very minor impl. contributions, but from my (non-expert) view, I like that (1) it installs easily (also on a MacBook) and (2) no header files. Felt much easier to get started with than, e.g., C++. I never truly learned good .h/.cpp practices, and I could never get OpenMP/g++ working well

Also, it's in Rust! Tool available at github.com/aljpetri/isO...

As for results, isONclust3 handles a 37M reads PacBio dataset from a revio machine in under 10h while other algorithms fail (>256Gb mem or >120h runtime). On the other datasets, isONclust3 has comparable or better accuracy than the other benchmarked tools.

The algorithm follows isONclust's algorithm in the general structure (greedy minimizer matching) but adds three key concepts: high confidence minimizers, on-the-fly cluster information update, and iterative (post-)cluster merging.

The motivation to develop this algorithm came from the inability of other algorithms to process recent large datasets (10-100M reads) from Revio or PromethION machines.

De novo clustering of large long-read transcriptome datasets with isONclust3 AbstractMotivation. Long-read sequencing techniques can sequence transcripts from end to end, greatly improving our ability to study the transcription proc

@alexanderjpetri.bsky.social's isONclust3 algorithm is now published doi.org/10.1093/bioi.... isONclust3 performs de novo clustering of long-read cDNA sequencing data. A key step in reference-free transcriptome analysis.

@tolyan.bsky.social is our very last speaker, on randstrobes ( high sensitivity seeds ) and their evolution the multi context seeds