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Sanger Sequencing Files Submission

🔴 In a nutshell: Sanger file ➡️ Allele submission + Isolate submission

Table of contents

📚 For further details on submission procedures, please visit BIGSdb documentation website.

Why making an isolate submission ?

Making an isolate submission is mandatory whether you want to define a new allele or a new MLST profile. This submission is used to collect isolate metadata. If a new allele/MLST profile is defined, the isolate submission also makes the link between the new nomenclature elements and the isolate they originate from.

⚠️ Warning : Please note that if you make an allele/profile submission without an isolate submission, your allele/profile submission will be considered incomplete and will be closed.

How to make an isolate submission ?

  1. Log onto the database you want to submit data to (ex: Klebsiella, Corynebacterium,...).
  2. Go to the Isolates and genomes database.
    button_isolate_database
  3. Click on SUBMISSIONS to access the submission panel.
    submission_button_submission_panel
  4. Select the isolates submission type.
    submission_type_isolate_link
  5. Download a template by clicking on one of the following buttons.
    button_download_template
  6. Fill in the template with your info. Copy/paste the template's content into the box then click on SUBMIT.

Metadata fields description are available in the quick links table.
fill_informations_isolates 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.
button_finalize_submission

How to make an allele submission ?

Trimming sequences and file naming conventions

You can submit any number of new sequences for a single locus and related trace files.

  • 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)

Example: SB1_gapA_398509385_F.ab1 and SB1_gapA_398509385_R.ab1

⚠️ Warning : Please keep in mind that if any of the previously mentioned steps have not been followed, your submission will be considered incomplete and may be closed.

📌 Note : 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 effectively.

Allele Submission: step-by-step

  1. Log onto the database you want to submit in (ex : Klebsiella, Corynebacterium,...).
  2. Go to the Alleles and profiles database.
    button_alleles_database
  3. Click on SUBMISSIONS to access the submission.
    submission_button_submission_panel
  4. Select the alleles submission type.
    submission_type_allele
  5. Choose the locus for which you want to define a new allele, fill in the sequence details fields, provide your new allele sequence then click on SUBMIT.
    fill_informations_alleles
  6. Upload the Sanger chromatograms (Forward & Reverse) for each new allele submitted using the box provided
    button_upload
  7. Send your submission by clicking on FINALIZE SUBMISSION button_finalize_submission

How to make a profile submission ?

Multiple novel profiles can be provided as a single submission.

  1. Log onto the database you want to submit in (ex : Klebsiella, Corynebacterium,...).
  2. Go to the Alleles and profiles database.
    button_alleles_database
  3. Click on SUBMISSIONS to access the submission.
    submission_button_submission_panel
  4. Select the MLST profile submission type.
    submission_type_allele
  5. Download a template by clicking on one of the following buttons.
    button_download_template
  6. Fill in the template with your info. Copy/paste the template's content into the box then click on SUBMIT.

The metadata fields description for each database is available in the quick linkstable.
fill_informations_isolates
7. You will be redirected to a new page with a summary of the metadata you provided.
Make sure everything is correct and then finalize the submission by clicking on the corresponding button.
button_finalize_submission

Quick links

🦠 Organism Isolates Alleles MLST
Bordetella Metadata description
Submission page 		Submission page Submission page
Corynebacterium diphtheriae complex Metadata description
Submission page 		Submission page Submission page
Elizabethkingia Metadata description
Submission page 		Submission page Not Applicable
Escherichia coli Metadata description
Submission page 		Submission page Submission page
Klebsiella pneumoniae species complex Metadata description
Submission page 		Submission page Submission page
Staphylococcus epidermidis Metadata description
Submission page 		Submission page Not Applicable
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