My samples

Status of my samples

You can access information on samples submitted by your laboratory by selecting a status under My samples on the left sidebar:

• Warnings: samples that have a warning upon loading into the database (e.g. missing raw data file)
• Loaded: samples that have been successfully parsed and loaded into the SPSP database
• Processing: samples that are currently undergoing bioinformatics analyses
• Processed: samples that have completed the bioinformatics analysis, stratified by their quality. Note that only samples with quality Warning or Pass will be available to other SPSP users under View data.
• Public: samples that have been shared to a public repository (e.g. to the European Nucleotide Archive)
• Exports: your list of exports (see documentation below for Exports).

The resulting table can be sorted, filtered and visible columns can be adjusted using the Display button.

Exports

Sharing consensus genomes or raw data with colleagues is possible with the Export feature, which is fully controlled by the data owners. It is possible to export metadata, consensus genomes and raw data of your samples with status Processed or Public.This will generate a temporary export link (valid for 7 days) that you will receive by email and that you can forward to colleagues with whom you wish to share the data (they will need access to SPSP).

Start by filtering the data that you wish to export, then click on Export next to the Display button.

This will open a pop up window where you can select what data to include in the Export.

Click on Create to finalise the export process. You will receive an email with a download link once the export has been generated. The link remains valid for 7 days. It is possible to prolong the validity of a link by clicking Exports on the left sidebar, and then selecting Resend email with link under “…” of the corresponding Export.