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.

The procedure for submitting data for curation were updated on Mai 03, 2024. Please consult them before making a new submission. If any questions, contact us.

Submission procedure for whole genome assembly

Submission procedure

NB. Note that the images used to illustrate the submission process are based on the Klebsiella database. However, it is important to note that the process is similar for each of the other databases. Although the specifics may vary according to the database used, the fundamental steps remain the same.

Quality criteria for whole genome assembly

Before submitting genomes, please ensure that they meet the quality criteria defined for the bacterial group. The quality criteria for each bacterial group are available below:

Genomes type Submission

Once logged into the Isolates and genomes database for the pertinent bacterial group, click on "SUBMISSIONS" to access the submission panel and choose the "genomes" submission type.


Isolates & genomes database submission section Genome type submission

Alternatively, you can access directly to the genomes type submission page for each database using the links below. Please, be sure to read the submission procedure in its entirety.

Please use the template provided to supply information about the isolate and the names of the assembly files. A guidance note is available in the headers of the template to help you to complete the metadata fields. Alternatively, a description of the fields for each database is available below.

Please label your assembly files exactly as the assembly_filename of the template and in accordance to the isolate name. For example, if the isolate name is ATCC13883 in the template, the assembly file should be ATCC13883.fas. The suffixes .fa, .fasta or .fna are also acceptable.

Once you've filled in the template, please copy/paste the information into the box provided, then click "SUBMIT".

Fill genomes meta data

You will be redirected to a new page for uploading assembly files.

NB. Note that you cannot upload more than 32 MB of files at a time. If you have more than 32 MB of files you will need to upload all your files in several batches of 32 MB or less.

Upload assembly files

Once all the files have been uploaded, please finalize the submission by clicking on the corresponding button.

Finalize genomes submission

NB. The submitted genomes can be embargoed. If you wish your genomic sequences to become public at a later stage, for example, when a publication is accepted (or no later than one year after submission, typically); please indicate this via the Messages box of the submission page.

Edit on GitLab