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giphy-ip.bsky.social
GIPhy
@giphy-ip.bsky.social
15 followers 10 following 20 posts

Genome Informatics & Phylogenetics | giphy.pasteur.fr | CRBIP | crbip.pasteur.fr | Institut Pasteur

#phylogenetics #systematics #taxonomy #genomics #bioinformatics #algorithmics
Posts Replies Media Videos
giphy-ip.bsky.social
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
GIPhy / AlienDiscover · GitLab
Inferring alien oligonucleotides (adapter, primer, index, barcode, ...) without any prior or external knowledge
gitlab.pasteur.fr
December 2, 2025 at 4:57 AM
giphy-ip.bsky.social
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
GIPhy / ASSU · GitLab
Assembling SSU
gitlab.pasteur.fr
December 1, 2025 at 6:06 PM
Reposted by GIPhy
sylvainbrisse.bsky.social
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 👇
Life Identification Numbers: A bacterial strain nomenclature approach
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
doi.org
November 30, 2025 at 7:51 PM
giphy-ip.bsky.social
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
Contribution of maternal gut carriage to neonatal acquisition of extended-spectrum beta-lactamase-producing Enterobacterales in Madagascar and Cambodia - Nature Communications
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
November 25, 2025 at 4:52 PM
Reposted by GIPhy
chcrestani.bsky.social
📢 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
November 7, 2025 at 3:53 PM
giphy-ip.bsky.social
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
September 18, 2025 at 8:45 AM
giphy-ip.bsky.social
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
August 21, 2025 at 2:35 PM
giphy-ip.bsky.social
FQsum: high-speed estimate of a full range of descriptive statistics from #FASTQ files
#bioinformatics #short-reads #long-reads

gitlab.pasteur.fr/GIPhy/FQsum
FQsum performances
August 3, 2025 at 10:41 AM
giphy-ip.bsky.social
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 / AlienDiscover · GitLab
Inferring alien oligonucleotides (adapters, primers, ...) from FASTQ file
gitlab.pasteur.fr
July 28, 2025 at 9:14 AM
giphy-ip.bsky.social
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
GIPhy / AlienTrimmer · GitLab
Fast trimming of sequencing reads
gitlab.pasteur.fr
July 21, 2025 at 2:41 PM
giphy-ip.bsky.social
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
Véronique LEGRAND / ROCK · GitLab
Institut Pasteur Gitlab
gitlab.pasteur.fr
July 1, 2025 at 11:57 AM
giphy-ip.bsky.social
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
wgetENAHTS
June 25, 2025 at 12:32 PM
Reposted by GIPhy
sylvainbrisse.bsky.social
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
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...
research.pasteur.fr
June 12, 2025 at 2:46 PM
Reposted by GIPhy
pasteur.fr
🇪🇺 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).
EU Reference Laboratories for public health
EU Reference Laboratories for public health
health.ec.europa.eu
June 6, 2025 at 7:34 AM
giphy-ip.bsky.social
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 👍
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...
www.nature.com
May 28, 2025 at 10:55 AM
giphy-ip.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
fq2dna (FASTQ 2 de novo assembly)
March 13, 2025 at 8:11 AM
giphy-ip.bsky.social
100th birthday of Margaret Dayhoff, mother of the science of #bioinformatics

www.nature.com/articles/s43588-025-00784-y
Celebrating a pioneer in bioinformatics - Nature Computational Science
In honor of the 100th birthday of Margaret Dayhoff, we spotlight her footprint in the field of bioinformatics.
www.nature.com
March 12, 2025 at 6:49 AM
giphy-ip.bsky.social
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
fqCleanER (fastq Cleaning and Enhancing Routine)
March 11, 2025 at 1:49 PM
giphy-ip.bsky.social
A new agreement with Springer Nature to advance OA publishing in France!!!

www.springernature.com/gp/open-scie...
Open access agreement for France | Open science | Springer Nature___small_youtube___
If you are a corresponding author affiliated with a participating French institution within Couperin, the agreement reached means you can publish your article open access (OA) with fees covered by you...
www.springernature.com
March 3, 2025 at 2:41 PM
giphy-ip.bsky.social
The 50th characterized Pseudoalteromonas species is named P. holothuriae
#taxonomy #phylogenetics #genomics

www.microbiologyresearch.org/content/jour...
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...
www.microbiologyresearch.org
February 26, 2025 at 4:50 PM
giphy-ip.bsky.social
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
Véronique LEGRAND / ROCK · GitLab
Institut Pasteur Gitlab
gitlab.pasteur.fr
February 17, 2025 at 12:13 PM
Reposted by GIPhy
jobim2025.bsky.social
❗❗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 !
Journées Ouvertes en Biologie, Informatique et Mathématiques - 2025
jobim2025.labri.fr
February 3, 2025 at 2:57 PM
giphy-ip.bsky.social
Cohnella rhizoplanae, a newly described species with potential plant-beneficial function contributing abilities

link.springer.com/article/10.1...
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...
link.springer.com
January 17, 2025 at 7:56 AM
giphy-ip.bsky.social
Kaarinaea lacus, a newly described cyanobacteria type species

www.sciencedirect.com/science/arti...
January 16, 2025 at 1:40 PM
giphy-ip.bsky.social
An unexpected Bacteroides fragilis Division I isolate co-harboring cepA and cfiA antimicrobial resistance genes

doi.org/10.1093/jac/...
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
doi.org
January 16, 2025 at 9:49 AM