Institut Pasteur MLST databases and software

This page provides access to genotypic data for Bordetella isolates based on Multilocus Sequence Typing (MLST) and core genome MLST (cgMLST). See references for more details.

bordetellaMLST@pasteur.fr

Data access policy note: since January 1st, 2025, registration and authentication are mandatory to access all data curated after this date, either via the web interface or via the application programming interface (API authentication help link). Please contact us if you have any questions.

Alleles & profiles database

The typing database contains nomenclature - allele definitions that provide an identifier for every unique allele sequence, and MLST profiles that index each unique combination of alleles with a sequence type (ST).

Isolates & genomes database

The isolate database consists of isolate records containing provenance and phenotype information linked to molecular typing information. These records may also include genome assemblies.

Data submission

Before contacting the curators, please download and read carefully the files below:

Submission of data for curation

Quality criteria for whole genome assembly

Metadata fields description

Infographic

Template for Bordetella genomes

We appreciate if you can recognize our efforts in the acknowledgments section of your publications:

We thank the Institut Pasteur teams for the curation and maintenance of BIGSdb-Pasteur databases at https://bigsdb.pasteur.fr/.

Curators access

Data Curation is performed on a voluntary basis and is based on a community effort.

Sequences and Profiles

Isolates

Other Information

BIGSdb manual

Primers used for amplification and sequencing (MLST)

Overlapping loci

Edit on GitLab