SeqSphere+ manages and stores

• procedure details (e.g., laboratory details, assembly parameters, and target QC)
• procedure statistics (e.g., reads, assembly and cgMLST statistics),
• genotyping results (e.g., MLST ST, cgMLST CT, or allelic profiles), and
• epidemiological metadata (e.g., sample ID, collection date).

For each sample the metadata field values are shown in the Epi tabs (Epi Basic, Epi Source, Epi Characteristic, Epi Species Specific), in the Procedure tab, and in the Results tab of the sample overview panel. All metadata field values can be exported to a MS Excel or CSV file that contains a single row with all values per sample.

Part of the laboratory procedure detail fields is compliant with EBI ENA/NCBI SRA (using a controlled vocabulary) as SeqSphere+ uses these by ENA required fields for raw read data submission to ENA. Laboratory and assembly procedure details are usually the same for a batch of sequences and SeqSphere+ users can define the content of these field data once and attach them to a bunch of samples, for example by defining in a pipeline script default Procedure Details. The SeqSphere+ software always generates and stores target scan procedure details and target QC procedure details automatically. The procedure statistics (read, assembly, and cgMLST) are sample specific and these fields cannot be filled-in by the user manually. Those fields are filled automatically by the SeqSphere+ software as far as they are available. Laboratory and assembly procedure details and procedure statistics can be exported and imported via CSV-files or proprietary SPEC files.

Metadata can be imported interactively using menu commands or automatically in the pipeline. See page Import of Metadata for details.

A description of the interactive export of metadata can be found on page Export Metadata. Metadata can be automatically exported from pipeline runs.