SPSP

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Instructions for new groups and users ​

Version 7 - August 2024

💡 CHECKLIST of information to send to spsp-support@sib.swiss

  • Institutional/company IP range
  • Public ssh key associated to your lab accession number
  • ENA center name (available from ENA profile page)

Set up the SPSP transfer tool ​

  • Please send us your institutional/company IP range. This is needed to whitelist you on the SPSP secure servers.
  • Please download SendCrypt to transfer data to SPSP and configure it following the instructions.
  • Please send us your public ssh key associated to your LAB_XXXX accession number (the lab accession number should have been sent to you upon acceptance of registration).
  • After your first batch submission, please send an email to SPSP support to ensure that everything went smoothly.

Get the metadata template file ​

Please use the data-specific SPSP metadata template file to describe the data submitted to SPSP. You can use either the Excel (.xlsx) template or a simple TSV (.tsv) using the variable names as header. In any case, please make sure to carefully read the explanations and examples provided for each field in the Excel template prior to starting. The latest version of the template and instructions is available here. In case of questions, please contact SPSP support.

Share your ENA center name for data exports ​

SPSP submits data and minimal pseudonymized metadata to GISAID (if relevant) and ENA.

⚠️ Note: no sensitive data are communicated to external public repositories. Please make sure not to use any sensitive sample identifier in the strain name.

SPSP metadata fields communicated to external public repositories (if provided):

  • strain_name
  • location (Continent/Country/Canton)
  • isolation_source_description (host)
  • sequencing_platform
  • assembly_method
  • raw_dataset_coverage
  • collecting_lab_name
  • reporting_lab_name
  • authors

Please send to SPSP support:

  • ENA center name:
    • If you don’t have an ENA Webin account yet: please register here and then follow the bullet point just below.
    • If/once you have an ENA Webin account: You can find (and edit if you wish) your ENA center name by [logging to your Webin account] (https://www.ebi.ac.uk/ena/submit/webin/login) and then going to "Edit account info > center name". Please make sure to have a center name that identifies your lab uniquely, e.g. Institute name, City, Switzerland. We need your center name to submit on your behalf to ENA.

Summary of data processing upon submission ​

  • If you are using the GUI version of SendCrypt, you will have access to a log of all your submissions on SendCrypt.
  • On the [SPSP private frontend] (https://spsp.sib.swiss), you can view all your submissions as well as any issues upon loading them into the database. The SPSP Support Team will inform you in case of warnings or errors in your batch submission.
  • Upon submission, SPSP will:
  • Automatically quality-control the data when loading them in the SPSP database.
  • Manually curate the data if needed, in case of warnings or errors (SPSP Support Team might contact you).
  • Automatically analyze the data using a pathogen/data-specific bioinformatics pipeline.
  • Automatically share pseudonymized data to international repositories.
    • If relevant for the data-type and not done already by the lab, SPSP will submit the consensus sequence to GISAID.
      • Upon request by GISAID, the SPSP Support Team might contact you about potential frameshifts of stop codons in your sequences.

      💡 Tip : It is also possible to include with your batch submission a frameshift_report.csv generated by [smallgenomeutilities] (https://github.com/cbg-ethz/smallgenomeutilities/releases) (ETHZ). Please make sure to add an additional column "strain_name" to the report. If such a file exists, SPSP will parse it automatically and ensure rapid release of your sequences on GISAID. Please contact SPSP support for more information.

    • If relevant for the data-type and if not done already by the lab, SPSP will submit the raw genomic data and consensus sequence to the ENA on your behalf.
  • If an agreement with federal authorities exist for the pathogen/data, automatically share with them the required data.
  • Automatically send you a submission-status report email just after midnight with all your submissions of that day, including external GISAID/ENA identifiers.
  • Data can be browsed on the SPSP Public portal (de-identified data only) or on the SPSP Secure Private portal.

Contact ​

For any question or suggestion on SPSP, please send an email to SPSP support.