# SURVEILLANCE COMMAND LINE

python /PATH/TO/reportree.py -a Se_beone_alleles.tsv -m Se_beone_metadata.tsv -out Se_beone_GT -l cgMLST_Salmonella_enterica_chewie-NS.txt --loci-called 0.95 -thr 1,2,5,10,25,100,500,1000 --analysis grapetree --nomenclature-file ../run_last_week/Se_beone_last_week_GT_partitions.tsv --nomenclature-code 500,100,25,10 --columns_summary_report MLST_ST,Predicted_serotype,Country,n_Country,Source,n_Source,first_seq_date,last_seq_date,timespan_days



# SURVEILLANCE COMMAND LINE WITH ZOOM-IN ON CLUSTERS OF INTEREST

python /PATH/TO/reportree.py -a Se_beone_alleles.tsv -m Se_beone_metadata.tsv -out Se_beone_GT -l cgMLST_Salmonella_enterica_chewie-NS.txt --loci-called 0.95 -thr 1,2,5,10,25,100,500,1000 --analysis grapetree --nomenclature-file ../run_last_week/Se_beone_last_week_GT_partitions.tsv --nomenclature-code 500,100,25,10 --columns_summary_report MLST_ST,Predicted_serotype,Country,n_Country,Source,n_Source,first_seq_date,last_seq_date,timespan_days --sample_of_interest ERR10442916 --zoom-cluster-of-interest 5 --site-inclusion 1.0 --unzip



# COMMAND LINE REQUESTING STABILITY REGIONS

python /PATH/TO/reportree.py -a Se_beone_alleles.tsv -m Se_beone_metadata.tsv -out Se_beone_GT -l cgMLST_Salmonella_enterica_chewie-NS.txt --loci-called 0.95 --analysis grapetree --nomenclature-file ../run_last_week/Se_beone_last_week_GT_partitions.tsv --nomenclature-code 500,100,25,10 --columns_summary_report MLST_ST,Predicted_serotype,Country,n_Country,Source,n_Source,first_seq_date,last_seq_date,timespan_days --partitions2report stability_regions 
