Tutorial

Tip: Remember to run conda activate ncov-recombinant first!

1. Preview the steps that are going to be run.

   snakemake --profile profiles/tutorial --dryrun
   

2. Run the workflow.

   snakemake --profile profiles/tutorial
   

3. Explore the Output.

   • Slides | results/tutorial/report/report.pptx

   • Tables^* | results/tutorial/report/report.xlsx

   • Plots

     • Reporting Period (default: last 16 weeks): results/tutorial/plots

     • All sequences: results/tutorial/plots_historical

   • Breakpoints

     • By parental clade: results/tutorial/plots_historical/breakpoints_clade.png

     • By parental lineage: results/tutorial/plots_historical/breakpoints_lineage.png

   • Alleles ^† | results/tutorial/sc2rf/recombinants.ansi.txt

^* Individual tables are available as TSV linelists in results/tutorial/linelists.
^† Visualize sc2rf mutations with less -S or Visual Studio ANSI Colors.