Antoine Limasset
@npmalfoy.bsky.social
CNRS researcher in bioinformatics
Lille, France (Bonsai team).
I develop efficient computational methods to analyze massive sequencing data, creating scalable tools for genomics, transcriptomics, and metagenomics.
https://malfoy.github.io/
Lille, France (Bonsai team).
I develop efficient computational methods to analyze massive sequencing data, creating scalable tools for genomics, transcriptomics, and metagenomics.
https://malfoy.github.io/
Reposted by Antoine Limasset
The morning session concluded with a talk by Megan Le: DeKnot—Local haplotype-resolved assembly with k-syncmer-
based multiplex De Bruijn graphs
The goal is to perform local haplotype assembly by iteratively growing lists of k’ consecutive closed syncmers.
based multiplex De Bruijn graphs
The goal is to perform local haplotype assembly by iteratively growing lists of k’ consecutive closed syncmers.
November 6, 2025 at 6:46 PM
The morning session concluded with a talk by Megan Le: DeKnot—Local haplotype-resolved assembly with k-syncmer-
based multiplex De Bruijn graphs
The goal is to perform local haplotype assembly by iteratively growing lists of k’ consecutive closed syncmers.
based multiplex De Bruijn graphs
The goal is to perform local haplotype assembly by iteratively growing lists of k’ consecutive closed syncmers.
Reposted by Antoine Limasset
Haonan Wu gives a talk on "A k-mer-based estimator of the substitution rate between repetitive sequences"
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
November 6, 2025 at 4:38 PM
Haonan Wu gives a talk on "A k-mer-based estimator of the substitution rate between repetitive sequences"
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
I really think this taps into a very masculinist, performative streak that’s rampant in programming culture and should be called out more.
a man in a suit and tie is laughing while holding a glass of wine .
ALT: a man in a suit and tie is laughing while holding a glass of wine .
media.tenor.com
November 7, 2025 at 10:21 AM
I really think this taps into a very masculinist, performative streak that’s rampant in programming culture and should be called out more.
Well, that’s nice, but I’m no alpha 10x coder, never will be, and that’s not even my goal.
I genuinely love programming, but being “fast” at it should not have the importance it’s currently given. (Don’t get me wrong, programming contests are fun.)
I genuinely love programming, but being “fast” at it should not have the importance it’s currently given. (Don’t get me wrong, programming contests are fun.)
a cartoon of homer simpson typing on a keyboard with the words " the ultra pro programmers be like " above him
ALT: a cartoon of homer simpson typing on a keyboard with the words " the ultra pro programmers be like " above him
media.tenor.com
November 7, 2025 at 10:21 AM
Well, that’s nice, but I’m no alpha 10x coder, never will be, and that’s not even my goal.
I genuinely love programming, but being “fast” at it should not have the importance it’s currently given. (Don’t get me wrong, programming contests are fun.)
I genuinely love programming, but being “fast” at it should not have the importance it’s currently given. (Don’t get me wrong, programming contests are fun.)
Just to be clear, such tasks are not challenging or interesting, but they still take a lot of time (and energy!)
I often hear it’s a skill issue, that a REAL programmer does it on the fly faster than you can even read it, without errors!
I often hear it’s a skill issue, that a REAL programmer does it on the fly faster than you can even read it, without errors!
a black and white photo of a shirtless man with a beard smiling
ALT: a black and white photo of a shirtless man with a beard smiling
media.tenor.com
November 7, 2025 at 10:21 AM
Just to be clear, such tasks are not challenging or interesting, but they still take a lot of time (and energy!)
I often hear it’s a skill issue, that a REAL programmer does it on the fly faster than you can even read it, without errors!
I often hear it’s a skill issue, that a REAL programmer does it on the fly faster than you can even read it, without errors!
Reposted by Antoine Limasset
Stay tuned: We are now running Metapuccino on SRA’s 1 million human transcriptomes.
November 2, 2025 at 10:14 AM
Stay tuned: We are now running Metapuccino on SRA’s 1 million human transcriptomes.