Preparing the working directory

Minimal set of files and directories expected in the working directory.

NE_nCoV_rapid/
│
├── pre-analyses/
   ├── provision.json 		→ FASTA file with the latest genomes from GISAID
   ├── new_genomes.fasta 		→ FASTA file with newly sequenced genomes
   ├── metadata_nextstrain.tsv	        → metadata downloaded from GISAID
   └── Sequencing.xlsx 			→ Custom lab metadata file