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 proprietary SPEC files.

Epidemiological metadata can be typed in per sample via the sample overview panel or imported via a MS Excel or CSV file. Most of those data fields are modeled according the Global Microbial Identifier (GMI)/NCBI minimum epidemiological data requirements (e.g., FDA GenomTrakr or CDC are using these fields). The focus of these requirements lies obviously on the three classical epidemiological dimensions, i.e., place, time, and ‘person’ information. In contrast to the procedure detail and statistic data fields, a SeqSphere+ user can create next to the default epidemiological data fields as many as wished additional epidemiological data fields by defining a customized database scheme for storing epidemiological data.