Table 1.

SIEGA features and description.

Feature	Description
Interface	With different subsections to facilitate the analysis: Sample Status information on each sample, including the quality control status Metadata information needed for sample and study traceability Application control information on the status and results of the pipeline of analysis Results detailed overview of the results obtained for any sample Flexible Table allows merging of any variety of result tables, metadata, or statuses for complex representation of results
User management	Access permission structure allowing users and group with many options to share data across users and groups
Data upload	Comma-separated values (CSV) file for metadata Fastq R1 and R2 files for each sample
Data processing and quality control	Quality control information on the result of each application is reportes (green: good, yellow: fair, red: poor)
Data traceability	Each sequenced sample has a distinctive identifier, used for associating relevant metadata
Automatic reporting	A report is generated for each sample including: MLST cgMLST Serotyping outcomes Antimicrobial resistance genes Virulence genes Plasmids A phylogenetic tree with the most related samples
Customized phylogenetic analysis	All existing tables can be combined using a wizard (flexible table) that enables the creation of combined tables with relevant data for each case, from which phylogenetic trees can be generated
Alert system	Automatic alerts based on various criteria can be established: Allelic distances Specific sequence type match Serotype predicted Presence of antimicrobial resistance genes Presence of virulence genes