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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
Note that the images used to illustrate the submission process are based on the Klebsiella database however the process is similar for other databases.
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:| 🦠 Organism | Quality Criteria |
|---|---|
| Bordetella | Quality Criteria |
| Corynebacterium diphtheriae complex | Quality Criteria |
| Elizabethkingia | Quality Criteria |
| Escherichia coli | Quality Criteria |
| Klebsiella pneumoniae species complex | Quality Criteria |
| Leptospira | Quality Criteria |
| Listeria monocytogenes | Quality Criteria |
| Staphylococcus epidermidis | Quality Criteria |
Steps to make an isolate Submission
1. Log onto the database in which you want to submit (ex : Klebsiella , Corynebacterium,...)2. Go to the Isolates and genomes database
3. Click on SUBMISSIONS to access the submission
4. Choose the genomes submission type.
Alternatively, you can directly access database-specific submission pages using the links in the table.
5. Download the template by clicking on one of the following buttons.
6. Fill in the templates & copy/paste your info into the box then click on SUBMIT.The metadata description for each database is available in the table on the right.
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 accepted.
7. Upload the assembly files for each isolate using the box provided.
Missing assembly files will be displayed in red. Please make sure that all your genomes have been uploaded correctly before proceeding to the next step.
| Assembly file missing | Assembly file uploaded |
|---|---|
 |
 |
8.Make sure everything is correct and that all genomes have been uploaded and then finalize the submission by clicking on the corresponding button.
| 🦠 Organism | 📝 Metadata description | 📥 Submission page |
|---|---|---|
| Bordetella | Database Fields | Submission page |
| Corynebacterium diphtheriae complex | Database Fields | Submission page |
| Elizabethkingia | Database Fields | Submission page |
| Escherichia coli | Database Fields | Submission page |
| Klebsiella pneumoniae species complex | Database Fields | Submission page |
| Leptospira | Database Fields | Submission page |
| Listeria monocytogenes | Database Fields | Submission page |
| Staphylococcus epidermidis | Database Fields | Submission page |
🔒 Embargo request
If you need an embargo period (e.g., prior to publication) you can, when submitting your data, request an embargo by ticking the "Request embargo" box and selecting the desired embargo period.The request for the initial embargo period cannot exceed 24 months.
Once the embargo date has passed, the data will be made public immediately, It will no longer be possible to make it private again.