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.
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:
- Bordetella
- Corynebacterium diphtheriae complex
- Elizabethkingia
- Escherichia coli
- Klebsiella pneumoniae species complex
- Leptospira
- Listeria monocytogenes
- Staphylococcus epidermidis
Genomes type Submission
- Once logged into the Isolates and genomes database for the pertinent bacterial group, click on "SUBMISSIONS" to access the submission panel.
- Choose the "genomes" submission type.
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.
- Bordetella
- Corynebacterium diphtheriae complex
- Elizabethkingia
- Escherichia coli
- Klebsiella pneumoniae species complex
- Leptospira
- Listeria monocytogenes
- Staphylococcus epidermidis
- 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.
- Bordetella
- Corynebacterium diphtheriae complex
- Elizabethkingia
- Escherichia coli
- Klebsiella pneumoniae species complex
- Leptospira
- Listeria monocytogenes
- Staphylococcus epidermidis
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".
- 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.
- Once all the files have been uploaded, please finalize the submission by clicking on the corresponding button.
Embargo request
If you would like to request an embargo period to keep your data private for some time (e.g., prior to your study’s publication), you can do so when submitting your data, by ticking the "Request embargo" box and selecting the desired embargo duration. The initial embargo period cannot exceed 24 months (2 years).
NB Once the embargo period has ended, the data will be made public automatically. Once public, the data cannot be made private again.