Screening for presence of genes in short read samples → 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 samplesfull genome shotgun sequencing→ PanPhlAn screen for new strains of a species ( E. coli) and identify the strain specific gene set |
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