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Igor Martayan

@imartayan.bsky.social

740 followers 310 following 59 posts

PhD student in algorithmic bioinformatics at @bonsaiseqbioinfo.bsky.social. Interested in randomized algorithms and space-efficient data structures https://igor.martayan.org

igor.martayan.org

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Igor Martayan @imartayan.bsky.social · Jan 29

I'm glad to announce that the simd-minimizers library is out! 🧬🖥️
@curiouscoding.nl and I have been optimizing the computation of minimizers down to the smallest detail.
The result is an order of magnitude faster than existing methods ; processing an entire human genome takes only 4s on my laptop! 🧵

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jan 28

SimdMinimizers: Computing random minimizers, fast https://www.biorxiv.org/content/10.1101/2025.01.27.634998v1

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Reposted by Igor Martayan

Bede Constantinides @bedec.bsky.social · 1d

"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary."
engineering.fb.com/2025/10/06/d...

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Reposted by Igor Martayan

Signal @signal.org · 5d

We are alarmed by reports that Germany is on the verge of a catastrophic about-face, reversing its longstanding and principled opposition to the EU’s Chat Control proposal which, if passed, could spell the end of the right to privacy in Europe. signal.org/blog/pdfs/ge...

signal.org

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RECOMB Conference Series @recombconf.bsky.social · 6d

#RECOMB2026 is now accepting submissions and we'd love to see your best work!

📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025

📜 More info: recomb.org/recomb2026/call_for_papers.html

RECOMB 2026 | CALL FOR PAPERS

Call For Papers

recomb.org

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Reposted by Igor Martayan

Xian Chang @xian-chang.bsky.social · 6d

🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 6d

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1

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Reposted by Igor Martayan

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 7d

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching https://www.biorxiv.org/content/10.1101/2025.09.29.679204v1

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Reposted by Igor Martayan

Ragnar {Groot Koerkamp} @curiouscoding.nl · 7d

Looking for people to test the latest version of simd-sketch.

It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).

'cargo install simd-sketch' is right there under your fingertips ;)

github.com/RagnarGrootK...

GitHub - RagnarGrootKoerkamp/simd-sketch: Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.

Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate. - RagnarGrootKoerkamp/simd-sketch

github.com

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Reposted by Igor Martayan

EMBL-EBI @ebi.embl.org · 8d

There are millions of openly available microbial genomes, but searching them can be slow.

Until now 🥁

Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more.

www.ebi.ac.uk/about/news/r...
🦠

How to rapidly search the world’s microbial DNA

By making the world’s microbial DNA easier to explore, LexicMap helps researchers track outbreaks, study antibiotic resistance, and understand microbial diversity.

www.ebi.ac.uk

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Reposted by Igor Martayan

David Monniaux @monniauxd.bsky.social · 13d

Vous pouvez soutenir ma proposition à la Cour des Comptes d'examiner les marchés publics de voyagistes, notamment dans l'ESR :
participationcitoyenne.ccomptes.fr/processes/co...

Les marchés publics de voyagistes - Contributions - 2025 - Aidez-nous à enrichir notre programme de travail - Plateforme de participation de la Cour des Comptes

Corps de la contributionLes administrations et opérateurs publics, notamment ceux de l'enseignement supérieur et de la recherche, fond appel à des agences de voyage (FCM, TravelPlanet…) pour l'hôtelle...

participationcitoyenne.ccomptes.fr

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Reposted by Igor Martayan

RECOMB Conference Series @recombconf.bsky.social · 12d

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!

Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!

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Reposted by Igor Martayan

Adam Phillippy @aphillippy.bsky.social · 16d

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

www.biorxiv.org

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Igor Martayan @imartayan.bsky.social · 16d

Depends on how full it is I guess, negative queries are fast when you don't need probing

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Justin Wolfers @justinwolfers.bsky.social · 18d

Critical part of the President's new $100,000 charge for H1-B visas: The Administration can also offer a $100,000 discount to any person, company, or industry that it wants. Replacing rules with arbitrary discretion.

Want visas? You know who to call and who to flatter.

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Reposted by Igor Martayan

Ragnar {Groot Koerkamp} @curiouscoding.nl · 21d

Minimap2 is very much the hammer in
"When all you have is a hammer, everything looks like a nail."

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Reposted by Igor Martayan

Bede Constantinides @bedec.bsky.social · 26d

Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...

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Reposted by Igor Martayan

Zamin Iqbal @zaminiqbal.bsky.social · 28d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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Reposted by Igor Martayan

Jim Shaw @jimshaw.bsky.social · Sep 7

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

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

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Reposted by Igor Martayan

Mikaël Salson @mikael-salson.univ-lille.fr · Sep 4

A wonderful day for @bonsaiseqbioinfo.bsky.social, with @camillemrcht.bsky.social's and @npmalfoy.bsky.social's HDR defenses.
Congrats for the amazing work!

It's a great chance for the team to have you both!

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Reposted by Igor Martayan

Giulio Ermanno Pibiri @jermp.bsky.social · Sep 1

We are glad to announce that the next workshop “Data Structures in Bioinformatics” (DSB 2026) will take place in Venice, Italy, on *February 18-19*, 2026. dsb-meeting.github.io/DSB2026/ Book the dates! #DSB26

DSB 2026 Venice - February 18-19

Workshop Data Structures in Bioinformatics

dsb-meeting.github.io

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Reposted by Igor Martayan

Bede Constantinides @bedec.bsky.social · Aug 11

📣 Deacon 0.8.0 available on Bioconda
- Much faster search and depletion through improved work distribution on multicore systems. My fastq.gz benchmark now runs at 400Mbp/s on Apple M1.
- Dual default match thresholds for greater accuracy

Details: github.com/bede/deacon/...

1k downloads! 🐥

Release 0.8.0 · bede/deacon

Faster filtering on multicore systems through improved work allocation using the Paraseq library (@noamteyssier). Filtering at >1Gbp/s is possible with uncompressed long sequences, and >500Mbp/s is...

github.com

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Reposted by Igor Martayan

Ragnar {Groot Koerkamp} @curiouscoding.nl · Aug 11

So, the heap I invented over the weekend was introduced as the quickheap by Navarro and Paredes around 2006!
Basically: on each pop, do just enough quicksort to find the smallest element.

My implementation (the 1st??) is 2x to 4x faster than d-ary and binary heaps.

curiouscoding.nl/posts/quickh...

A grid of plots compaing the performance of a binary heap, 8-ary heap, 4-ary heap, quickheap, and radix heap, all taken from various rust crates.
The top 4 plots are for u32 values, the bottom 4 for u64 values.
Each column is a different type of input. The left is heapsort: insert n times then pop n times. The second column does groups of push followed by 4x (pop, push), and then the reverse. The last two columns have linearly/randomly increasing data.

On the first two data sets, the quickheap is by far the best, showing my less degradation of cache misses than the d-ary heaps.

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Jouni Sirén @jltsiren.bsky.social · Aug 8

There was a workshop on 25 years of the FM-index and the CSA after SEA. I would have liked to attend, but I had other commitments. The invited speakers were Giovanni Manzini and Roberto Grossi, as the other purpose of the workshop was to present them Festschrifts for their 60th birthdays. 1/6

SEA 2025

regindex.github.io

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Ragnar {Groot Koerkamp} @curiouscoding.nl · Aug 6

Little writeup on the speed of fasta parsers, at last.

Basically: both needletail and paraseq are process input linearly, and thus have a limit around 4 GB/s.

By giving each thread its own slice of the input file, we're limited by RAM bandwidth instead :)

curiouscoding.nl/posts/fasta-...

With 3 threads, the middle thread processes the reads starting in the middle third of the fasta file.

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Reposted by Igor Martayan

Rob Patro @robp.bsky.social · Aug 5

🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3

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Igor Martayan @imartayan.bsky.social · Aug 4

Congrats! Is it publicly available?

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Rob Patro @robp.bsky.social · Aug 3

I talk a lot about Rust for building high-perf (& even non-perf critical) software, & scientific software in particular. I often discuss what's interesting to me, but wanted to offer the chance to those interested for me to answer their questions about Rust in science. Fire away with questions!🧬🖥️

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