downloads new versions of the curated SARS-CoV-2 lineage file and barcodes
db_name:string
The name of the database directory
barcodes
${db_name}/usher_barcodes.csv:file
File containing lineage defining barcodes
*barcodes.csv
lineages_topology
${db_name}/lineages.yml:file
File containing the lineage topology
*lineages.yml
lineages_meta
${db_name}/curated_lineages.json:file
File containing lineage metadata that correspond to barcodes
*lineages.json
versions
versions.yml:file
File containing software versions
versions.yml
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
