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Assembly Submission Guidelines

Table of contents

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

Why making an assembly submission ?

If you have already submitted an isolate to BIGSdb Pasteur, you can update it with a whole genome assembly file. To proceed, you need the isolate ID.

How to make an assembly 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 assembly submission type
    Alternatively, you can directly access database-specific submission pages using the links in the table.
    submission_type_assembly
  5. Fill in the box with the following tab delimited information : Isolate ID Isolate name Sequencing method Assembly filename
    Allowed file formats : .fa, .fasta, .fna
    Allowed sequencing methods values : 454, Illumina, Ion Torrent, PacBio, Oxford Nanopore, Sanger, Solexa, SOLiD, other, unknown
    fill_informations_assembly
    Click on SUBMIT.
  6. Upload the assembly files for each isolate using the box provided.
    You can drag and drop your files up to 32MB at a time, but one submission can contain up to 500 genomes.
    button_upload
    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 missingAssembly file uploaded
    Missing assembly (assembly submission) Assembly uploaded (assembly submission)

    Metrics that do not fit the preferred range value will have a pink background as a warning. They still can be submitted.

  7. Make sure everything is correct and that all genomes files have been properly uploaded. Finalize the submission by clicking on the corresponding button.
    button_finalize_submission

Quick links

🦠 Organism 📥 Submission page
Bordetella Submission page
Corynebacterium diphtheriae complex Submission page
Elizabethkingia Submission page
Escherichia coli Submission page
Klebsiella pneumoniae species complex Submission page
Leptospira Submission page
Listeria monocytogenes Submission page
Staphylococcus epidermidis Submission page
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