AlienDiscover: 🆕 v0.3 available to infer alien oligos (adapter, index, barcode, heteropolymer, ...) from #FASTQ files ✅ new confidence score for each inferred #long-read alien oligos ✅ ability to filter out #long-read alien oligos with low score ✅ still fast gitlab.pasteur.fr/GIPhy/AlienDiscover

ASSU: 🆕 version 1.2 for quickly ASSembling SSU (16S) rRNA segments using short HTS reads derived from prokaryote WGS. #bioinformatics #FASTQ #16S #rRNA ➡️ new preset options for better sensitivity 🧬 ➡️ up-to-date SSU reference databank 🦠 gitlab.pasteur.fr/GIPhy/ASSU research.pasteur.fr/en/tool/assu

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

Thrilled to share the new @natcomms.nature.com paper, challenging the debatable paradigm that maternal carriage is the primary source of early neonatal ESBL-PE colonization in low- and middle-income countries @pasteur.fr 🚼 🌍 🌏 research.pasteur.fr/en/b/1AV1 dx.doi.org/10.1038/s41467-025-65352-4

📢 Save the Date! The 2nd Nanopore Users Day will take place 🗓️10 March 2026 at the Duclaux Amphitheater, Institut Pasteur (Paris). This edition will be open to external participants! 👉 More details and registration info coming soon! @chloebaum.bsky.social @pasteur.fr @nanoporetech.com

A nice illustration of the usefulness of our tool #MSTclust for handling bacterial population structures by @sylvainbrisse.bsky.social during #IMMEMXIV in Porto 🇵🇹 gitlab.pasteur.fr/GIPhy/MSTclust

Welcome to Thalassoporum mexicanum 🇲🇽 and Tumidithrix helvetica 🇨🇭, two Cyanobacteriota species 🦠 successfully characterized by @aniketsaraf.bsky.social et al. #phylogenetics #genomics #taxonomy @pasteur.fr @microbiologysociety.org research.pasteur.fr/en/b/18sC dx.doi.org/10.1099/ijsem.0.006869

FQsum: high-speed estimate of a full range of descriptive statistics from #FASTQ files #bioinformatics #short-reads #long-reads gitlab.pasteur.fr/GIPhy/FQsum

AlienDiscover: 🆕 version 0.2 available inference of alien oligonucleotides (adapter, primer, index, barcode, ...) without any prior nor external knowledge ➡️ still accurate on #short-read #FASTQ files ➡️ now able to deal with #long-read #FASTQ files ➡️ very fast gitlab.pasteur.fr/GIPhy/AlienDiscover

AlienTrimmer: 🆕 version 3.0 available @sylvainbrisse.bsky.social @pasteur.fr ☑️ now able to clip low-residue content regions ☑️ deal with Phred scores up to 95 ☑️ still one of the fastest #FASTQ clipping/trimming tool gitlab.pasteur.fr/GIPhy/AlienTrimmer research.pasteur.fr/en/software/alientrimmer

ROCK (Reducing Over-Covering K-mers): 🆕 version 3.0 #bioinformatics #FASTQ #LongReads ➡️ now able to quickly perform digital normalization on long-read data files gitlab.pasteur.fr/vlegrand/ROCK research.pasteur.fr/en/software/rock

wgetENAHTS: 🆕 version 4.3 multi-threaded #FASTQ file downloading from the European Nucleotide Archive (ENA) repository ➡️ now deals with the last ENA file report format gitlab.pasteur.fr/GIPhy/wgetENAHTS

The BIGSdb-Pasteur project, running under my supervision since 20 years, is looking for a project manager - great opportunity to contribute to this high-profile international resource in the field of reference strain taxonomies, genomic epidemiology and antimicrobial resistance surveillance

🇪🇺 The Institut Pasteur is pleased to announce that two research units, "Lyssavirus, Epidemiology and Neuropathology" and "Biodiversity and Epidemiology of Bacterial Pathogens," have been designated as European Union Reference Laboratories (EURLs).

Deep insight into the genomic population structure and evolution of the zoonotic pathogen Corynebacterium ulcerans 🦠 www.nature.com/articles/s41467-025-60065-0 Congratulations to @chcrestani.bsky.social and @sylvainbrisse.bsky.social 👍

fq2dna: 🆕 version 25.03 #genomics #FASTQ #bioinformatics ✔️ new accuracy index ✔️ compatible with up-to-date dependency versions ✔️ several bugs fixed gitlab.pasteur.fr/GIPhy/fq2dna research.pasteur.fr/en/tool/fq2dna

100th birthday of Margaret Dayhoff, mother of the science of #bioinformatics www.nature.com/articles/s43588-025-00784-y

fqCleanER: 🆕 version 25.03 #bioinformatics #FASTQ ➡️ updated list of alien oligos ➡️ updated trap and TMPDIR handling ➡️ several fixed minor bugs gitlab.pasteur.fr/GIPhy/fqCleanER research.pasteur.fr/en/tool/fqcleaner

A new agreement with Springer Nature to advance OA publishing in France!!! www.springernature.com/gp/open-scie...

The 50th characterized Pseudoalteromonas species is named P. holothuriae #taxonomy #phylogenetics #genomics www.microbiologyresearch.org/content/jour...

ROCK (Reducing Over-Covering K-mers): new version 2.1 #bioinformatics #FASTQ => fixed bug that (rarely) occurs when processing very large FASTQ files gitlab.pasteur.fr/vlegrand/ROCK research.pasteur.fr/en/software/rock

❗❗BREAKING NEWS❗❗ Les soumissions pour #JOBIM2025 sont ouvertes ! 😱 💡Articles longs, posters, démos, etc ; de nombreux formats sont attendus. Les consignes détailles seront accessibles sur le site de #JOBIM2025 ➡️ jobim2025.labri.fr ⏳ Les soumissions fermeront le 31 mars, alors faîtes vite !

Cohnella rhizoplanae, a newly described species with potential plant-beneficial function contributing abilities link.springer.com/article/10.1...

Kaarinaea lacus, a newly described cyanobacteria type species www.sciencedirect.com/science/arti...

An unexpected Bacteroides fragilis Division I isolate co-harboring cepA and cfiA antimicrobial resistance genes doi.org/10.1093/jac/...