usage.rst

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.