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.
]]>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 <a href="mailto:[email protected]">contact us</a> if you have any questions.
]]>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 <a href="mailto:[email protected]">contact us</a> 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, <a href="mailto:[email protected]">contact us</a>.
]]>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, <a href="mailto:[email protected]">contact us</a>.
]]>
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
]]>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
]]>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.
]]>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
]]>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.
]]>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
]]>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.
]]>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
]]>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
]]>
Genomic library of Bordetella - Bridel et al. preprint has been published in biorXiv!
A unified library of Bordetella genomes has been set-up by merging previously existing Oxford and Pasteur databases, importing genomes from public repositories, and developing harmonized genotyping schemes. A genus-wide cgMLST genotyping scheme was developed and 18 putative novel species found. Specific schemes were developed to define antigenic, virulence and macrolide resistance profiles.
Access the Bordetella genomic library at https://bigsdb.pasteur.fr/bordetella/
The genomic platform provides an expandable resource for unified genotyping of Bordetella strains and will hopefully facilitate collective evolutionary and epidemiological understanding of the reemergence of whooping cough and other Bordetella infections.
]]>Genomic library of Bordetella - Bridel et al. preprint has been published in biorXiv!
A unified library of Bordetella genomes has been set-up by merging previously existing Oxford and Pasteur databases, importing genomes from public repositories, and developing harmonized genotyping schemes. A genus-wide cgMLST genotyping scheme was developed and 18 putative novel species found. Specific schemes were developed to define antigenic, virulence and macrolide resistance profiles.
Access the Bordetella genomic library at https://bigsdb.pasteur.fr/bordetella/
The genomic platform provides an expandable resource for unified genotyping of Bordetella strains and will hopefully facilitate collective evolutionary and epidemiological understanding of the reemergence of whooping cough and other Bordetella infections.
]]>
A new website is welcoming you, we hope you appreciate. Don't forget to star your favorite bacterias !
If you find any issue, do not hesitate to contact us.
]]>A new website is welcoming you, we hope you appreciate. Don't forget to star your favorite bacterias !
If you find any issue, do not hesitate to contact us.
]]>
The MLST strain nomenclature service for diphtheriae/ulcerans strains is now available. This nomenclature has been earlier mantained by Martin Maiden and Keith Jolley at the University of Oxford, and now migrated by Sebastien Bridel to BIGSdb-Pasteur https://bigsdb.pasteur.fr/diphtheria/.
]]>The MLST strain nomenclature service for diphtheriae/ulcerans strains is now available. This nomenclature has been earlier mantained by Martin Maiden and Keith Jolley at the University of Oxford, and now migrated by Sebastien Bridel to BIGSdb-Pasteur https://bigsdb.pasteur.fr/diphtheria/.
]]>
BIGSdb pasteur is now in 1.32.2:
- a customizable dashboard allows you to visualize key information such as geographical distribution, or number of isolates available in the database
- the Microreact plugin have been updated following breaking changes introduced on the Microreact website
More information are available here
]]>BIGSdb pasteur is now in 1.32.2:
- a customizable dashboard allows you to visualize key information such as geographical distribution, or number of isolates available in the database
- the Microreact plugin have been updated following breaking changes introduced on the Microreact website
More information are available here
]]>
A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae - Hennart et al. preprint has been published on bioRxiv!
A proposal to build genomic taxonomies of bacterial strains using a dual approach combining single linkage clustering and life identification numbers into a single cgMLST-based multilevel classification system.
Here, the 634-loci strict core genome MLST (scgMLSTv1) initially identified in Bialek-Davenet et al, 2014 was reassessed, and an improved cgMLST scheme of 629-loci (scgMLST629_S) for K. pneumoniae Species Complex genotyping was provided.
This Hennart et al. 629-loci cgMLST scheme has been incorporated into the BIGSdb-Klebsiella nomenclature server.
]]>A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae - Hennart et al. preprint has been published on bioRxiv!
A proposal to build genomic taxonomies of bacterial strains using a dual approach combining single linkage clustering and life identification numbers into a single cgMLST-based multilevel classification system.
Here, the 634-loci strict core genome MLST (scgMLSTv1) initially identified in Bialek-Davenet et al, 2014 was reassessed, and an improved cgMLST scheme of 629-loci (scgMLST629_S) for K. pneumoniae Species Complex genotyping was provided.
This Hennart et al. 629-loci cgMLST scheme has been incorporated into the BIGSdb-Klebsiella nomenclature server.
]]>
BIGSdb pasteur is now in 1.30.0:
- enabling support of iTOL
More information are available here
]]>BIGSdb pasteur is now in 1.30.0:
- enabling support of iTOL
More information are available here
]]>