Igor Martayan

Just submitted my PhD thesis on algorithms for fast, large-scale k-mer-based sequence analysis. It's now available to read at phd.martayan.org Take a look and feel free to share! #Bioinformatics #PhDone

Sebastiano Vigna: PHastR: Faster Minimal Perfect Hashing with Rotated Layouts https://arxiv.org/abs/2610.17833 https://arxiv.org/pdf/2610.17833 https://arxiv.org/html/2610.17833

Skani (github.com/bluenote-157...) is now v0.4.0! Big performance update: **~2.5x faster** and ~30-40% less RAM for average nucleotide identity (ANI) comparison of genomes. The database format has changed (breaks forward compatibility; watch out!).

(Thread) New Logan preprint 🥳 www.biorxiv.org/content/10.6...! We sketched all the metagenomes of Logan1.0 and released the sketches. These sketches allow quick content comparison with any/all metagenomes of Logan. Cool applications in the paper and hopefully many others we did not foresee yet 😀

Great work by @rfaure.bsky.social and others, happy to see it out!

A very important message from Omer Reingold to our TCS community, especially us (arg, already) senior researchers: "snap out of it." Please, digest, and share. theorydish.blog/2026/09/29/s...

Tangentially, @jermp.bsky.social also points out @recombconf.bsky.social is listed as B tier in CORE portal.core.edu.au/conf-ranks/?.... This is something that we should figure out how to address. RECOMB is a premiere conference in comp bio, & it is highly selective. It is `A` tier without question.

Ok comp. bio / bioinformatics / genomics friends. Let's talk about @recombconf.bsky.social and, specifically, the way in which the "proceedings" have evolved. This seems like something that we, as a community, should address. RECOMB now has no "published" proceedings in the classic sense.

The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)

I've been working on processing pseudoalignments from different tools to make downstream methods agnostic to the pseudoaligner choice, give it a try if you use themisto / fulgor / etc: docs.rs/ahda Also provides compression, conversion, and set operations.

Happy to announce that I'll defend my PhD next Friday (Sept 4) at 2pm CEST! There will be a live stream on Zoom, just send me a message if you'd like to join!

Obviously this doesn't scale, but I chose to send this junior researcher a (hopefully polite) email with some of my thoughts (written hastily in 30 minutes, not polished). More practicing mathematicians & researchers should advocate for the culture they want, so here's my bit.

Xilin Tang (Cornell University), Yuqi Mai (Cornell University), William Kuszmaul (Carnegie Mellon University), Alex Conway (Cornell Tech): Succinct and Fast Tiny Pointer Hash Tables https://arxiv.org/abs/2607.28892 https://arxiv.org/pdf/2607.28892 https://arxiv.org/html/2607.28892

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools

Ever wanted to quickly check host content of DNA sequences? bede.im/sapiometer

My secret 4th ALGO paper is out! We show a tight space lower on non-minimal k-perfect hash functions, generalize PtrHash into a non-minimal k-PHF, and then use it to develop a hash set implementation that is up to 1.6x faster than other hash sets! With Stefan {Hermann, Walzer} and Peter Sanders

Lossless compression of k-mer matrices enabling random row access https://www.biorxiv.org/content/10.64898/2026.07.03.736306v1

Binary search and and set operations on compacted k-mer lists https://www.biorxiv.org/content/10.64898/2026.06.29.735436v1

synpact: accurate, memory-light PacBio HiFi read mapping via a hierarchy of locally-consistent syncmer blocks https://www.biorxiv.org/content/10.64898/2026.06.28.735066v1

Francisco Olivares, Gonzalo Navarro: Practical Linear-Time Computation of Smallest Suffixient Sets https://arxiv.org/abs/2606.31034 https://arxiv.org/pdf/2606.31034 https://arxiv.org/html/2606.31034

In other news: Great SEA talk by Nathaniel Brown on Orbit, an efficient implementation of the move structure for run-length encoded permutations. Also, congrats on winning a best paper award with this work!

Oh my, a GPU implementation of Super Bloom filters!

Happy to see that K2Rmini was recommended today by PCI Mathematical & Computational Biology. "quickly evaluate whether an arbitrary sequence has a number of k-mer [of interest] matches above or below a threshold." by @imartayan.bsky.social and colleagues: www.biorxiv.org/content/10.1...

Does your designed active site already exist in nature? Is an uncharacterized protein hiding a catalytic site or a pocket? Folddisco answers both, searching millions of structures for a 3D motif in seconds. @natbiotech.nature.com 🧬 📄 www.nature.com/articles/s41... 🧵1/7👇

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

Glad to announce that our new long-read metagenomic SNP caller, SNooPy, is published in NAR! Existing long-read SNP callers are not designed for metagenomic data, check out our new solution 👉https://academic.oup.com/nar/article/54/10/gkag556/8700491 @narjournal.bsky.social

Now also on arxiv arxiv.org/abs/2606.01190

Congrats to @leoackermann.bsky.social on winning RECOMB's best poster award for his work on compressing pairwise distance matrices! Check it out here: lacker.gitlab.io/pdf/research...

Memory-safe high-performance sequence mapping with rammap https://www.biorxiv.org/content/10.64898/2026.05.26.726289v1

Fast Set Operations for Compact k-mer Sets https://www.biorxiv.org/content/10.64898/2026.05.24.727514v1

Is anyone attending #RECOMB2026 with a talk in the Sequencing 2 session who would be willing to switch slots with a talk in Sequencing 1 a day earlier? We’d be very grateful. Please reach out if you might be willing to do this!

More and better human assemblies. Now annotate them to the minute. Special kudos @trhyker.bsky.social @jnalanko.bsky.social and @florisbarthel.bsky.social

wow — the preprint host, arxiv, is banning authors for a year if they submit papers with hallucinated citations 🤖

Me in group meeting update: Sassy was accepted at Bioinformatics, and Barbell should be accepted soon. Me at end of group meeting update: Both Sassy and Barbell are now accepted at Bioinformatics 🎉 Who will be the first to cite? All thanks to the wonderful work of @rickbitloo.bsky.social!!!

🔍 New paper in Bioinformatics Advances: "Kaminari: A frugal colored index for approximate k-mer queries"  Read it here: https://doi.org/10.1093/bioadv/vbag120 Authors include: @yhhshb.bsky.social, @yoann.bsky.social, @robp.bsky.social, @pierrepeterlongo.bsky.social, @jermp.bsky.social

This is now published in Genome Research (doi.org/10.1101/gr.2...). Thank you everyone for your feedback and also the anonymous reviewers who helped to greatly improve the paper. I hope this becomes a useful resource for the community.

The RECOMB-Seq 2026 program is now available! Join us May 24–25 in Thessaloniki, Greece, for two days of cutting-edge biological sequence analysis, with keynotes by Camille Marchet (CNRS) and Manolis Kellis (MIT). Full schedule: recomb-seq.github.io/seq2026/prog... #RECOMBseq

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. arxiv.org/abs/2604.25681 with Marvin Williams and Johannes Breitling:

New blog post! I use ntHash all the time to hash k-mers, yet it turns out it has some unexpected flaws (collision propagation, bias on leading zeros...). The good news: each of them can be fixed! igor.martayan.org/posts/breaki...

Turns out that the usual NtHash is not as random as one might think?!?! At least not for minimizers. Seq-hash (and simd-minimizers) already has this fixed by default ;) github.com/rust-seq/seq...

New blog post! I use ntHash all the time to hash k-mers, yet it turns out it has some unexpected flaws (collision propagation, bias on leading zeros...). The good news: each of them can be fixed! igor.martayan.org/posts/breaki...

The fastest way to match characters on ARM processors? https://lemire.me/blog/2026/04/19/the-fastest-way-to-match-characters-on-arm-processors/

I think this blog post comes closest to my current thinking on AI than any other I've read: fransskarman.com/im_not_using...

I'm not looking forward to a future where all the tools are being vibe-rewritten into languages people don't want to learn. Who will maintain all this? The original maintainers won't. It's not the language they were comfortable with. Does the prompter understand the tool well enough?