Tools‎ > ‎

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