scientific-infectious-disease

You can perform WGS-based typing by providing pathogen genome data in FASTQ or FASTA formats. The pipeline processes WGS data to execute MLST, cgMLST, and SNP typing for lineage tracing during outbreak investigations.

Yes, the pipeline detects AMR genes and resistance profiles from sequencing data. This AMR detection applies molecular typing workflows to identify resistance genes and inform treatment strategies during an outbreak.

You can run compartment models with configurable parameters to simulate pathogen spread. The pipeline executes SIR and SEIR models to forecast outbreak size and evaluate interventions based on integrated epidemiology data.

The best way to combine molecular typing and phylogenetics for outbreak investigations is using an integrated genomics pipeline. It constructs phylogenies from WGS data and infers transmission networks to identify transmission routes during hospital outbreaks.

Yes, the outbreak analysis pipeline requires pathogen genome data in FASTQ or FASTA formats. You must provide sequencing data in these formats to run the end-to-end pipeline for typing results, phylogenies, and transmission estimates.