De nouvelles familles de #coronavirus découvertes. pasteur.fr/fr/journal-rec…

Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads go.nature.com/35bCOL1

After a long wait, the latest in large-scale indexing from Fatemeh Almodaresi, @prashn_25, Jamshed Khan, @CSIdiotSavant, Rob Johnson, Mike Ferdman & I is published:academic.oup.com/bioinformatics… (preprint biorxiv.org/content/10.110…). This work shows how to make Mantis incrementally updatable. 1/

Out today: another companion methods paper from the Telomere-to-Telomere (T2T) consortium. Winnowmap2 enables better long read mapping and more accurate variant calling in repetitive regions of the genome. nature.com/articles/s4159…

Pairwise alignment is traditionally thought to take a lot of memory (query × sequence length), but we've just demonstrated that the actual bound is linear in sequence divergence. Amazingly, this comes at no runtime cost relative to a standard WFA! 🌊∿↝

hifiasm-meta offers a metagenome assembler that makes use of highly accurate long-read data. Xiaowen Feng Daniel Portik Heng Li nature.com/articles/s4159…

EBAME7 microbial ecogenomics workshop applications are open: maignienlab.gitlab.io/ebame7/ Brest, 🇫🇷, Oct. 24-Nov. 4 2022. Join us to learn more about omics data analysis methods for microbial ecology and evolution. Two weeks packed with lectures, tutorials in the beautiful Brest Bay.

Eventually! CheckM2 is there! It also performs well in predicting genome completeness of CPR and DPANN! One grain of salt though: The software was only benchmarked against the lab’s previous version CheckM1, not against all the other tools out there… biorxiv.org/content/10.110…

In this new Bioinformatics Application Note, we introduce a file format named KFF for efficiently storing kmers on disk. academic.oup.com/bioinformatics…

🇪🇺 4️⃣ scientifiques travaillant à l’Institut Pasteur reçoivent un European Research Council (ERC) Consolidator Grant ↘️ pasteur.fr/fr/journal-rec…

Tired of hairballs in your assembly graphs? We are excited to present stRainy - our new approach for metagenomic strain deconvolution using long reads! biorxiv.org/content/10.110…

The construction of large cohorts human pangenome graphs is a challenging task. We selected 5 different state-of-the art tools that generate variation graphs or De Bruijn graphs and used them to construct a human pangenome of 104 high-quality human haplotype assemblies. (1/4)

Very happy to present metaMDBG, a new assembler for long accurate metagenomics reads (e.g. PacBio HiFi)!

Camila Duitama (@camiladuitama1) successfully defended her PhD, on pioneering work for ancient metagenome DNA content analysis using large k-mer matrices. Co-advised with Hugues Richard and Riccardo Vicedomini. Congrats! Proud of your achievements :)

This year, GenScale is organizing the #SeqBIM 2024 workshop in Rennes, Nov 28-29! Don't miss the chance to present your work on sequences. 🗓️ Submission deadline: Oct 17 🔑 Keynotes: Kristoffer Sahlin & Zsuzsanna Lipták 📝 Register by Nov 14 🔗 More info: seqbim.cnrs.fr/seqbim-2024

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. Mile Sikic, Riccardo Vicedomini, Krešimir Križanović 🔗biorxiv.org/content/10.110… 1/9