WF_3_5_SNP_Phylo.md

Workflow 3.5 Script

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Creates SNP heatmap and Phylogenetic Tree

WF_3_5_SNP_Phylo.py

• frun_WF_3_5()
  • Calls run_docker, parse_AMR from helper file

WF_3_5_helper.py

• run_docker()

  • Calls on join_paired_end_reads and run_SNPCreation to create docker commands
  • Runs staphb/lyvese docker to create SNP heat map creation and build Phylogentic tree

• join_paired_end_reads()

  • Creates docker command to shuffle paired-end reads
  • Return docker command string

• run_SNPCreation()

  • Creates docker command to run SNP heat map creation and build Phylogentic tree
  • Return docker command string