PATH-SAFE analyses

Organism	Step	Tool/Pipeline name	Purpose	Output
All	Genome Assembly	EToKi pipeline	Assemble reads from FASTQs into FASTA	Genome Sequence, Assembly Statistics
All	Species assignment	Speciator	Ensure that the correct analyses are performed	Species (listed in Genome Report)
All	Sequence Typing - MLST	MLST	Assign MLST code for reporting.	MLST profile
All	Sequence Typing - cgMLST	cgMLST	Produce cgMLST profiles for use in context search clustering & finding HierCC code	cgMLST profile
All	Context searching	cgMLST Single-linkage Clustering	Find genomes similar enough to indicate possible transmission event or outbreak	Similar genomes getting added to the Search/ Collection
All	Plasmid Inc Typing	Inctyper	identify the contigs containing an Inc reference gene	Inc reference genes
All	Predicting AMR	ResFinder	Detecting known AMR genes & variants; prediction of phenotype from genotype	Antibiograms, AMR-related markers
S. enterica	Serotyping	SISTR & SeqSero2	Identify serotypes	Serovar
E. coli	Serotyping	ECTyper	Identify serotypes	Serovar
E. coli	Virulence	STECfinder & VirulenceFinder	Identify virulence factors	Virulence genes
L. monocytogenes	Virulence	Pasteur BIGSdb	Identify virulence factors	Virulence genes
E. coli	Lineage assignment	ClermonTyping	Assign strain phylotype uusing Clermont method	Phylogroup
E. coli S. enterica	Finding HierCC codes	hclink	Match the cgMLST profiles to the closest Enterobase HierCC code	HierCC code
S. enterica	Building trees	SNP-based Neighbour Joining	Visualise genome groupings and ancestral relationships between genomes	Dendrograms, tree-style representation of genome relationships
E. coli L. monocytogenes	Building trees	cgMLST-based Neighbour Joining	Visualise genome groupings and ancestral relationships between genomes	Dendrograms, tree-style representation of genome relationships