Pathogen screening

Screening for presence of genes in short read samples

full genome shotgun sequencing

→ MetaMLST

screen for presence of MLST genes or self-defined reference gene sequences

→ SRST2

screen for presence of MLST genes or self-defined reference gene sequences

→ ARIBA

screen for antibiotic resistance genes or MLST genes (local assembly based approach)

Screening for presence of genes in assembled contigs

→ ABRicate

screening of contigs for antimicrobial resistance or virulence genes

Screening for bacterial strains in short read samples

full genome shotgun sequencing

→ PanPhlAn

screen for new strains of a species (E. coli) and identify the strain specific gene set