GIPhy
@giphy-ip.bsky.social
12 followers 10 following 17 posts
Genome Informatics & Phylogenetics | giphy.pasteur.fr | CRBIP | crbip.pasteur.fr | Institut Pasteur #phylogenetics #systematics #taxonomy #genomics #bioinformatics #algorithmics
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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
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
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
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
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
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
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
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
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
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)
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)
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
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
giphy-ip.bsky.social
Kaarinaea lacus, a newly described cyanobacteria type species

www.sciencedirect.com/science/arti...