GIPhy

📢 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 performances

FQsum: high-speed estimate of a full range of descriptive statistics from #FASTQ files
#bioinformatics #short-reads #long-reads

gitlab.pasteur.fr/GIPhy/FQsum

GIPhy / AlienDiscover · GitLab Inferring alien oligonucleotides (adapters, primers, ...) from FASTQ file

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

GIPhy / AlienTrimmer · GitLab Fast trimming of sequencing reads

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

Véronique LEGRAND / ROCK · GitLab Institut Pasteur Gitlab

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

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

Project manager: Genomic taxonomy of bacterial strains, epidemiological surveillance and antimicrobial resistance - Research We are looking for a project manager to develop our activities around the genomic taxonomy of bacterial strains and the corresponding platform at https://bigsdb.pasteur.fr/. The project manager’s main...

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

EU Reference Laboratories for public health EU Reference Laboratories for public health

🇪🇺 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).

Microevolution and genomic epidemiology of the diphtheria-causing zoonotic pathogen Corynebacterium ulcerans - Nature Communications This study reveals prior undetected transmission events of Corynebacterium ulcerans, suggesting pets play an intermediary role between wildlife and humans. Two main sublineages were identified, showin...

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 (FASTQ 2 de novo assembly)

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 (fastq Cleaning and Enhancing Routine)

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...

Pseudoalteromonas holothuriae sp. nov., isolated from the sea cucumber Holothuria forskali Two motile bacterial strains, designated as cfHf56-1T and SW 252, were isolated from the coelomic fluid of Holothuria forskali and from the surrounding seawater at the animal sampling site, respective...

The 50th characterized Pseudoalteromonas species is named P. holothuriae
#taxonomy #phylogenetics #genomics

www.microbiologyresearch.org/content/jour...

Véronique LEGRAND / ROCK · GitLab Institut Pasteur Gitlab

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 !

Description of Cohnella rhizoplanae sp. nov., isolated from the root surface of soybean (Glycine max) - Antonie van Leeuwenhoek A Gram-staining-positive, aerobic bacterium, designated strain JJ-181 T, was isolated from the root surface of soybean. Based on the 16S rRNA gene sequence similarities, strain JJ-181 T was grouped in...

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...

Comment on: Co-occurrence of the cephalosporinase cepA and carbapenemase cfiA genes in a Bacteroides fragilis Division II strain: an unexpected finding We read with great interest the article by Valdezate et al.,1 which reports the first case of co-occurrence of the cepA and cfiA antimicrobial resistance g

An unexpected Bacteroides fragilis Division I isolate co-harboring cepA and cfiA antimicrobial resistance genes

doi.org/10.1093/jac/...