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
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...
Reposted by Igor Martayan
#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
📌 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
October 2, 2025 at 12:00 PM
#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
📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025
📜 More info: recomb.org/recomb2026/call_for_papers.html
Reposted by Igor Martayan
🦒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
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
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
October 2, 2025 at 6:28 AM
🦒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
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
Reposted by Igor Martayan
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
October 1, 2025 at 1:47 AM
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
Reposted by Igor Martayan
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...
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
October 1, 2025 at 2:38 PM
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...
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...
Reposted by Igor Martayan
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...
🦠
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
September 30, 2025 at 9:47 AM
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...
🦠
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...
🦠
Reposted by Igor Martayan
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...
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
September 25, 2025 at 10:28 AM
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...
participationcitoyenne.ccomptes.fr/processes/co...
Reposted by Igor Martayan
#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!
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!
September 26, 2025 at 3:03 PM
#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!
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!
Reposted by Igor Martayan
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
September 22, 2025 at 5:01 PM
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]
Reposted by Igor Martayan
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.
Want visas? You know who to call and who to flatter.
September 20, 2025 at 1:40 PM
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.
Want visas? You know who to call and who to flatter.