SNAPPy commands

This is a list of the implemented functionalities in SNAPPy:

• Basic subtyping:

  snakemake subtype_all
  

• Subtyping using n cpu cores:

  snakemake subtype_all --cores n
  

• Basic alignment:

  snakemake align_all
  

• Alignment using n cpu cores:

  snakemake align_all --cores n
  

• Clean the SNAPPy folder from previous runs outputs:

  snakemake delete_all_outputs
  

• Clean the SNAPPy folder from previous runs intermediate files (but not outputs):

  snakemake delete_interm_files
  

• Compress to a file and clean the SNAPPy folder from previous runs intermediate files (but not outputs):

  snakemake compress_and_del_inter_files
  

• Compress everything inside the SNAPPy folder to a file:

  snakemake compress_all
  

Note: Please note that SNAPPy is built on top of Snakemake, and therefore should retain all the functionalities of this pipeline software.