BIGSdb Pasteur is now in version 1.53.2. Here is an overview of the main new features introduced since version 1.52.2:

Easier API authentication with personal API keys

OAuth authentication has long been supported for the BIGSdb API, but many users found it complex to set up. A simpler alternative is now available: personal API keys. Each user can generate their own key directly from their BIGSdb profile. This key can then be used to authenticate API requests for downloading alleles and scheme data, without having to go through the full OAuth setup.

You can manage or revoke your key at any time from your user profile.

Improved password security

Several improvements have been made to password management:

• Passwords must now be at least 12 characters long.
• New complexity requirements can be enforced, including the use of special characters, upper-case and lower-case letters, and digits.
• The system now also checks that your username is not included in your password.

These changes help protect your account against unauthorised access.

Automatic database registration

New users no longer need to manually register their account with each individual database. When logging in for the first time and updating their password, users can now be automatically registered to all available databases, simplifying the onboarding experience.

FastTree support in the iTOL and Microreact plugins

The iTOL and Microreact plugins now support FastTree for generating approximate maximum likelihood phylogenetic trees. This makes it possible to analyse larger datasets than before, where previously only Clustal Neighbour-joining trees were available.

New LINvis features

The LINvis visualisation tool has been updated with several new features:

• Labelling of specific LIN prefixes: a popup list allows you to highlight and label particular LIN prefixes of interest directly on the visualisation.
• Label resizing controls: adjust label sizes to improve readability.
• Search by isolate ID or name: quickly locate and visualise specific isolates within the tree.
• Fit to visible vertical height: automatically adjust the view to fit the visible area of the screen.

More information is available here

Just out ! A novel version of diphtOscan is available at https://gitlab.pasteur.fr/BEBP/diphtoscan. It is easier to install and to use on local computers.

diphtOscan scans genomes of the Corynebacterium diphtheriae species complex and extracts information used for clinical and public health management, including diphtheria toxin and antimicrobial resistance genes, biovar, species and subtyping information. This release also supports authenticated access to BIGSdb-Pasteur’s diphtheria source database, ensuring access to the most recent genotype nomenclature.

The BIGSdb website is implementing new settings regarding data access. Data curated in 2025 (and later) will not be accessible for anonymous (non-logged-in users). If you wish to have access to data curated in 2025 and beyond, please register on the platform and login when using it. Note that access via the application programming interface (API) will also require authentication to access recent data (API authentication help link).

To ensure a smooth transition, anonymous data access will be periodically closed and opened from 1st October 2024 until the end of the year. For detailed planning, please follow this link.

On 1st January 2025, registration will be permanently mandatory to access data curated after the 31st of December 2024.

Please contact us if you have any questions.

The BIGSdb website Policy concerning the platform & data use agreement and the privacy notice of BIGSdb-Pasteur was updated on March 25, 2024. Please consult it before using the platform and the data. If any questions, contact us.

Large-scale Corynebacterium diphtheriae outbreak among migrant populations in Europe - phenotypic and genomic analysis - Hoefer et al. has been published in medRxiv!

A pan-European consortium was created to assess the clinical, epidemiological and microbiological features of this outbreak - BIGSdb Corynebacterium diphtheriae complex was used for sharing data between collaborators and analysing genome data.

The isolate-genome collection is avavailable in BIGSdb@Pasteur and accessible at the public project 2022_EuropeanWideReemergence_collection

BIGSdb pasteur is now in 1.42.6:

• This release introduces a new plugin that provides a wrapper for ReporTree - Mixão et al. 2023 Genome Med 15:43. See https://bigsdb.readthedocs.io/en/latest/data_analysis/reportree.html for details.
• Version 1.42 improves web-based sequence scanning by showing the position of the first in-frame stop codon for loci defined as 'complete CDS' and adds an option to separate the search for start and stop codons.

More information are available here

ReporTree added to BIGSdb-Pasteur

ReporTree is a pan-pathogen tool for automated and reproducible identification and characterization of genetic clusters developed by Mixão et al. (Genome Med, 2023)

This plugin creates the required input files for ReporTree and runs the tool to identify and characterize genetic clusters. A full description of the ReporTree plugin can be found in the BIGSdb manual.

Corynebacterium diphtheriae reemergence, genomic framework and bioinformatics tool to detect antimicrobial resistance and virulence - Hennart et al. preprint has been published in biorXiv!

The bioinformatics pipeline DIPHTOSCAN hepls to extract from genomes resistance and virulence genes, and medically relevant features including the toxin gene presence and disruption. The code source is available at https://gitlab.pasteur.fr/BEBP/diphtoscan

A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae - Hennart et al. 2022 has been published on Molecular Biology and Evolution!

LINcodes are now being defined in BIGSdb_Klebsiella based on the 629-loci cgMLST scheme. Find out more about LIN codes in BIGSdb here.

BIGSdb pasteur is now in 1.35.1:

• Version 1.34 provides support for LINcodes based on cgMLST schemes. See https://doi.org/10.1101/2021.07.26.453808 for more information about LINcodes.
• Version 1.35 adds support for alternative codon tables.

More information are available here

You can now follow the latest news posted in BIGSdb pasteur with your favorite news/rss feed aggregator.

Website for the #KlebNET Genomic Surveillance Platform is now live!

KlebNET-GSP provides the scientific community with a unified genomic surveillance platform with tailored analytics for the Klebsiella pneumoniae species complex (KpSC) wihle developing an international network of scientists involved in Klebsiella research and building capacity in genomics.

Check it out at klebnet.org

Don't forget to explore the News section for coming up events and training workshops, and to subscribe to the klebnet Google Group