Igor Martayan
@imartayan.bsky.social
PhD student in algorithmic bioinformatics at @bonsaiseqbioinfo.bsky.social.
Interested in randomized algorithms and space-efficient data structures
https://igor.martayan.org
Interested in randomized algorithms and space-efficient data structures
https://igor.martayan.org
Pinned
Igor Martayan
@imartayan.bsky.social
· Jan 29
SimdMinimizers: Computing random minimizers, fast https://www.biorxiv.org/content/10.1101/2025.01.27.634998v1
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! 🧵
@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! 🧵
Reposted by Igor Martayan
kache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming k-mer operations https://www.biorxiv.org/content/10.64898/2026.02.13.705625v1
February 17, 2026 at 5:47 AM
kache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming k-mer operations https://www.biorxiv.org/content/10.64898/2026.02.13.705625v1
Reposted by Igor Martayan
🚨UPCOMING DEADLINES🚨
RECOMB-CG: 13 February
RECOMB-RSG: 15 February
RECOMB-Privacy: 9 March
RECOMB-Seq: 12 March (abstract registration)
RECOMB-Arch: 12 March (abstract registration)
RECOMB-Genetics: 13 March
#RECOMB2026 #deadlines
RECOMB-CG: 13 February
RECOMB-RSG: 15 February
RECOMB-Privacy: 9 March
RECOMB-Seq: 12 March (abstract registration)
RECOMB-Arch: 12 March (abstract registration)
RECOMB-Genetics: 13 March
#RECOMB2026 #deadlines
February 5, 2026 at 8:41 PM
🚨UPCOMING DEADLINES🚨
RECOMB-CG: 13 February
RECOMB-RSG: 15 February
RECOMB-Privacy: 9 March
RECOMB-Seq: 12 March (abstract registration)
RECOMB-Arch: 12 March (abstract registration)
RECOMB-Genetics: 13 March
#RECOMB2026 #deadlines
RECOMB-CG: 13 February
RECOMB-RSG: 15 February
RECOMB-Privacy: 9 March
RECOMB-Seq: 12 March (abstract registration)
RECOMB-Arch: 12 March (abstract registration)
RECOMB-Genetics: 13 March
#RECOMB2026 #deadlines
Reposted by Igor Martayan
Preprint alert!
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
ZOR filters: fast and smaller than fuse filters
Probabilistic membership filters support fast approximate membership queries with a controlled false-positive probability $\varepsilon$ and are widely used across storage, analytics, networking, and b...
arxiv.org
February 4, 2026 at 12:28 PM
Preprint alert!
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
Reposted by Igor Martayan
So anyway:
BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth.
Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index.
github.com/RagnarGrootK...
raw.githubusercontent.com/RagnarGrootK...
BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth.
Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index.
github.com/RagnarGrootK...
raw.githubusercontent.com/RagnarGrootK...
February 4, 2026 at 1:24 AM
So anyway:
BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth.
Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index.
github.com/RagnarGrootK...
raw.githubusercontent.com/RagnarGrootK...
BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth.
Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index.
github.com/RagnarGrootK...
raw.githubusercontent.com/RagnarGrootK...
Reposted by Igor Martayan
Cool paper on representing a collection of sets via a spanning tree of their differences. This builds upon work by Bookstein ('91 )! as well as work we did in using this representation to compress color sets in Mantis MST. I think this repr. has many important applications! arxiv.org/pdf/2601.23240
arxiv.org
February 2, 2026 at 2:26 PM
Cool paper on representing a collection of sets via a spanning tree of their differences. This builds upon work by Bookstein ('91 )! as well as work we did in using this representation to compress color sets in Mantis MST. I think this repr. has many important applications! arxiv.org/pdf/2601.23240
Reposted by Igor Martayan
Generating minimum-density minimizers https://www.biorxiv.org/content/10.64898/2026.01.25.701585v1
January 28, 2026 at 10:46 AM
Generating minimum-density minimizers https://www.biorxiv.org/content/10.64898/2026.01.25.701585v1
Reposted by Igor Martayan
Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 22, 2026 at 9:15 PM
Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Igor Martayan
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
mirdita.org
January 20, 2026 at 11:07 AM
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
mirdita.org
Reposted by Igor Martayan
ahh, CMake, the best of what 1973 had to offer I'm sure
January 16, 2026 at 5:06 AM
ahh, CMake, the best of what 1973 had to offer I'm sure
Reposted by Igor Martayan
Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment https://www.biorxiv.org/content/10.64898/2025.12.17.694868v1
December 20, 2025 at 3:50 AM
Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment https://www.biorxiv.org/content/10.64898/2025.12.17.694868v1
Reposted by Igor Martayan
The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/
DSB 2026 Venice - February 18-19
Workshop Data Structures in Bioinformatics
dsb-meeting.github.io
December 10, 2025 at 2:29 PM
The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/
Reposted by Igor Martayan
github.com/bede/deacon
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
GitHub - bede/deacon: Fast DNA search and [host] depletion using minimizers
Fast DNA search and [host] depletion using minimizers - bede/deacon
github.com
December 3, 2025 at 7:40 PM
github.com/bede/deacon
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
Reposted by Igor Martayan
Preprint alert!
We introduce new ideas to revisit the notion of sampling with window guarantees, also known as minimizers.
A thread:
We introduce new ideas to revisit the notion of sampling with window guarantees, also known as minimizers.
A thread:
Minimizer Density revisited: Models and Multiminimizers https://www.biorxiv.org/content/10.1101/2025.11.21.689688v1
December 2, 2025 at 11:12 AM
Preprint alert!
We introduce new ideas to revisit the notion of sampling with window guarantees, also known as minimizers.
A thread:
We introduce new ideas to revisit the notion of sampling with window guarantees, also known as minimizers.
A thread:
Reposted by Igor Martayan
We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...).
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index
AbstractMotivation. The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many co
doi.org
November 27, 2025 at 11:27 AM
We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...).
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
Reposted by Igor Martayan
Okay, #SeqBim is over, let's get crackin' and speak about our recent preprint (joint work with @imartayan.bsky.social, Lucas Robidou, @camillemrcht.bsky.social and @npmalfoy.bsky.social)
1/
1/
November 27, 2025 at 10:18 AM
Okay, #SeqBim is over, let's get crackin' and speak about our recent preprint (joint work with @imartayan.bsky.social, Lucas Robidou, @camillemrcht.bsky.social and @npmalfoy.bsky.social)
1/
1/
Reposted by Igor Martayan
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 19, 2025 at 3:01 AM
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
Reposted by Igor Martayan
Bioinformatics x cybersecurity: Christina Boucher and her colleague Sara Rampazzi uncovered a basic yet critical vulnerability in MinIONs through the MinKNOW software bioengineer.org/portable-gen...
Portable Genetic Sequencer Security Vulnerabilities Could Endanger Personal
Portable genetic sequencers, particularly those manufactured by Oxford Nanopore Technologies, have revolutionized the field of genomics, making DNA sequencing more accessible and practical across the
bioengineer.org
November 12, 2025 at 7:44 AM
Bioinformatics x cybersecurity: Christina Boucher and her colleague Sara Rampazzi uncovered a basic yet critical vulnerability in MinIONs through the MinKNOW software bioengineer.org/portable-gen...
Reposted by Igor Martayan
The simplex algorithm is super efficient. 80 years of experience says it runs in linear time. Nobody can explain _why_ it is so fast.
We invented a new algorithm analysis framework to find out.
We invented a new algorithm analysis framework to find out.
Beyond Smoothed Analysis: Analyzing the Simplex Method by the Book
Narrowing the gap between theory and practice is a longstanding goal of the algorithm analysis community. To further progress our understanding of how algorithms work in practice, we propose a new alg...
arxiv.org
October 27, 2025 at 1:43 AM
The simplex algorithm is super efficient. 80 years of experience says it runs in linear time. Nobody can explain _why_ it is so fast.
We invented a new algorithm analysis framework to find out.
We invented a new algorithm analysis framework to find out.
Reposted by Igor Martayan
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out!
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 9:28 PM
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out!
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
Reposted by Igor Martayan
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes
Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi
github.com
October 21, 2025 at 8:00 PM
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
Reposted by Igor Martayan
Movi 2: Fast and Space-Efficient Queries on Pangenomes. #Pangenomes #SequenceQueries #Genomics #Bioinformatics @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 21, 2025 at 1:49 PM
Movi 2: Fast and Space-Efficient Queries on Pangenomes. #Pangenomes #SequenceQueries #Genomics #Bioinformatics @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Igor Martayan
So what's the equivalent of `perf record && perf report` on a MacBook?
I want to see the generated assembly and which lines are hot.
I want to see the generated assembly and which lines are hot.
October 11, 2025 at 1:48 PM
So what's the equivalent of `perf record && perf report` on a MacBook?
I want to see the generated assembly and which lines are hot.
I want to see the generated assembly and which lines are hot.
Reposted by Igor Martayan
Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ?
www.nature.com/articles/d41...
www.nature.com/articles/d41...
‘Google for DNA’ brings order to biology’s big data
MetaGraph compresses vast data archives into a search engine for scientists, opening up new frontiers of biological discovery.
www.nature.com
October 9, 2025 at 3:00 PM
Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ?
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Igor Martayan
"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...
engineering.fb.com/2025/10/06/d...
October 6, 2025 at 8:58 PM
"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...
engineering.fb.com/2025/10/06/d...
Reposted by Igor Martayan
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
October 3, 2025 at 4:14 PM
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...