Workflow for SC2 cluster investigations. TheiaCoV_Augur_Run will run Augur without a subsampling module using a modified version of The Broad Institute’s sarscov2_nextstrain WDL workflow to create an Auspice JSON file; output from the modified sarscov2_nextstrain workflow will also be used to infer SNP distances
This is a companion discussion topic for the original entry at github.com/theiagen/public_health_bioinformatics/TheiaCoV_Augur_Run_PHB