For impatient people

To run the full workflow you will need to execute at least 2 commands:

Import GISAID data:

1. `perl addToTable.pl --metadata metadata.tsv --seq sequences.fasta --nproc 16 --outfile linearDataSorted.txt `

Import Nexstrain data:

1. ` perl NextStrainToHaploCoV.pl --metadata metadata.tsv --outfile linearDataSorted.txt `

run the workflow:

2. `perl HaploCov.pl --file linearDataSorted.txt --locales italy.loc `

See the following sections for more details.