Roland Faure

🧵6/ 6
Since MSRs sketches are sequence, they are super easy to use. I think they could be useful for many other problems, e.g. SNP calling, pangenome graphs, indexing, etc.

🧵5/6
The sketching makes assembly extremely fast: a gut metagenome sample of 138Gbp of sequencing data was assembled in less that 2h and 10G RAM on 8 threads ⚡. And thanks to MSRs, *highly similar strains are not collapsed*

🧵4/6
Two key properties that make MSRs sketches really cool:
👉 They are alignable sequences: you can just feed them in existing assembler
👉 MSR sketches can *keep all the SNPs*, i.e. two highly similar sequences are (almost) always reduced to different sketches -> useful to separate similar strains

🧵3/ 6
MSRs have been defined by @lblassel.bsky.social @rayanchikhi.bsky.social and @pashadag.bsky.social in pmc.ncbi.nlm.nih.gov/articles/PMC....
Take a sequence, a value of k, and stream all k-mers through a function that output either a base or the empty character, and you got your sketch

🧵2/6
Conceptually, the assembler is on the same lines as metaMDBG:
1. sketching reads
2. assembly procedure on the sketches
3. reversing to base-space to obtain the final assembly
The main difference is the sketching scheme: we introduce *Mapping-friendly Sequence Reductions (MSR) sketching*

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...

Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6)
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

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

1 / N

Congrats! Nice results 🎉

I am happy to share our new preprint introducing MADRe - a pipeline for Metagenomic Assembly-Driven Database Reduction, enabling accurate and computationally efficient strain-level metagenomic classification.

🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1
1/9

Starting #RECOMBseq with @rayanchikhi.bsky.social 's keynote. Here stressing our responsibility as scientists to enable access to a common good: genomic data

Side note: you could, speaking purely theoretically, also fit every microbe onto an SD card, which is within the weight limit for a carrier pigeon. For some distances, it would be faster than the internet for transmitting sequence libraries
7/

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions a simple tool for listing conda environments with descriptions - rrwick/condaenvlist

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?

If so, you might this little project: github.com/rrwick/conda...

So glad to have participated in #DSB2025, what a great workshop! For some mysterious reason it was the first time I attended after 3 years of sequence research. Thanks to all participants & organizers 😃

Ragnar's made some incredible optimizations on the computation of minimizers, can't wait to see how these improvements will benefit bioinfo tools!

Really cool work!

Toy example of the AAAAAAA bucket associated to four super-k-mer turned into their interleaved representation.

Amazing ideas here www.biorxiv.org/content/bior... from
@yoann.bsky.social
and collaborators.

Reorganize minimizers to allow kmers dichotomic search. That's brilliant.

#bioinformatics 🧬🖥️

So glad to have successfully defended my Ph.D. last week 😀 Work on producing haplotype-resolved metagenomic assemblies using noisy long reads (HairSplitter) and high-fidelity long reads (Alice assembler, unpublished yet).
Thanks to my advisors Dominique Lavenier and Jean-François Flot ❤️

Congrats @firtinac.bsky.social ! I enjoyed thouroughly reading the BLEND paper 😄