Genome Sub-typing

subworkflows/local/subtype_genome

Steps

1. Species specific subtyping tools are launched according to the pipeline's Mash screen report.

2. Currently subtyping tools for E.coli, Salmonella, Listeria spp., Staphylococcus spp., Klebsiella spp. and Shigella spp. are supported.

3. Subtyping can be disabled from the command line by passing --skip_subtyping true on the command line.

NOTE If a sample cannot be subtyped, it merely passes through the pipeline and is not typed. A log message will instead be displayed notifying the user the sample cannot be typed.

Input

• Contig file (fasta) from the FinalAssembly dir
• This is the final contig file from the last step in the CleanAssemble workflow (taking into account any skip flags that have been used)
• Mash report from assembly speciation step in the CleanAssemble workflow

Output

• Subtyping
• ECTyper
  • SAMPLE
• SevenGeneMLST
• SISTR
• Etc...