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
The essay on using Life Identification Numbers (LIN) as a microbial strain nomenclature for epidemiological surveillance is now published in @plosbiology.org 🤩
Congratulations to @sylvainbrisse.bsky.social and all other co-authors 👍 👏
@pasteur.fr
AlienTrimmer v3.2 is now published in EMBnet.journal
🖥️ #FASTQ 🧬 @pasteur.fr
✅ efficient preset parameters for @nanoporetech.com data
✅ ultrafast when compiled using @graalvm.org native-image
journal.embnet.org/index.php/embnetjournal/article/view/1078
research.pasteur.fr/en/software/alientrimmer
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
Inferring alien oligonucleotides (adapter, primer, index, barcode, ...) without any prior or external knowledge
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
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
Among mother-neonate pairs in Madagascar and Cambodia, authors found maternal gut carriage explains only 16.5% of early neonatal extended-spectrum beta-lactamase Enterobacterales acquisition, question...
dx.doi.org
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 👇
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
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
sylvain Brisse
📢 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
GIPhy
Toward a unified taxonomy for bacterial strains
New essay in PLOS Biology explores the Life Identification Number system — a cgMLST‑based framework for stable, high‑resolution strain classification and global epidemiological tracking.
journals.plos.org/plosbiology/...
@sylvainbrisse.bsky.social
BIGSdb v1.52.1 has been released. This adds 2 new plugins for LIN code visualisation - LINtree (@giphy-ip.bsky.social) and LINvis. See github.com/kjolley/BIGS... for release notes. BIGSdb powers all the databases at @pubmlst.org and BIGSdb Pasteur.
Unified bacterial strain taxonomies are needed for coherent communication of findings in microbiological research. This Essay provides an overview of a novel bacterial strain taxonomy and describes ho...
