⛔ Maintenance: A BIGSdb-Pasteur maintenance is scheduled on Friday, July 04th and Saturday, July 05th. All services will be offline until late in the evening (Central European Time). During this period, the server and API will be unavailable. Please note that job submission not be available and all unfinished jobs will be killed. Sorry for any inconvenience. If any questions, contact us
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 Sanger Sequencing
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
Isolate Submission
The isolates submission is mandatory whether you want to define a new allele or a new MLST profile. This submission used to obtain the metadata linked to the isolate(s) and also to link the new allele/MLST profile to an isolate.Note that if you have made a submission for the definition of a new MLST allele/profile but the "isolates" submission has not been made, your submission will be considered incomplete and will be closed.
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 isolates 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.
7. You will be redirected to a new page with a summary of the informations you have provided. Make sure everything is correct and then finalize the submission by clicking on the corresponding button.
| 🦠 Organism | 📝 Metadata description | 📥 Submission page |
|---|---|---|
| Bordetella | Metadata description | Submission page |
| Corynebacterium diphtheriae complex | Metadata description | Submission page |
| Elizabethkingia | Metadata description | Submission page |
| Escherichia coli | Metadata description | Submission page |
| Klebsiella pneumoniae species complex | Metadata description | Submission page |
| Staphylococcus epidermidis | Metadata description | Submission page |
Allele Submission
You can submit any number of new sequences for a single locus and related trace files. Before making your submission, please ensure that you have completed the steps listed below :- Sequences should be trimmed to the correct start/end sites for the selected locus.
-
Trace files should be labeled according to the following model : {1}_{2}_{3}_{4}.{5}
- {1}: Strain code (avoiding special characters such as space, dot, slash, etc.).
- {2}: Gene name written exactly as in the database (e.g. gapA).
- {3}: Any additional information you would like.
- {4}: Forward Sequencing (F) or Reverse sequencing (R).
- {5}: File extension (.ab1 or .scf).
Note that if any of the previous steps have not been followed, your submission will be considered incomplete and the curators will be entitled to close it.
The discovery of a new allele is always linked to the discovery of a new MLST profile. Therefore, when submitting a new allele, it is recommended to submit the new MLST profile at the same time. This enables curators to group and process submissions more quickly.
Steps to make an Allele Submission
1. Log onto the database in which you want to submit (ex : Klebsiella , Corynebacterium,...)2. Go to the Alleles and profiles database
3. Click on SUBMISSIONS to access the submission
4. Choose the alleles submission type.
Alternatively, you can directly access database-specific submission pages using the links in the table.
5. Choose the locus for which you wish to define a new allele, fill in the Sequence details fields and the sequence of your new allele then click on SUBMIT
6. Upload the Sanger chromatograms (Forward & Reverse) for each new allele submitted using the box provided.
7. Finalize the submission by clicking on FINALIZE SUBMISSION!.
| 🦠 Organism | 📥 Submission page |
|---|---|
| Bordetella | Submission page |
| Corynebacterium diphtheriae complex | Submission page |
| Elizabethkingia | Submission page |
| Escherichia coli | Submission page |
| Klebsiella pneumoniae species complex | Submission page |
| Staphylococcus epidermidis | Submission page |
MLST Profile Submission
Multiple novel profiles can be provided as a single submission.Steps to make an MLST Profile Submission
1. Log onto the database in which you want to submit (ex : Klebsiella , Corynebacterium,...)2. Go to the Alleles and profiles database
3. Click on SUBMISSIONS to access the submission
4. Choose the MLST profile 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.
7. You will be redirected to a new page with a summary of the informations you have provided. Make sure everything is correct and then finalize the submission by clicking on the corresponding button.
| 🦠 Organism | 📥 Submission page |
|---|---|
| Bordetella | Submission page |
| Corynebacterium diphtheriae complex | Submission page |
| Escherichia coli | Submission page |
| Klebsiella pneumoniae species complex | Submission page |