Description

downloads new versions of the curated SARS-CoV-2 lineage file and barcodes

Input

name:type
description
pattern

db_name:string

The name of the database directory

Output

name:type
description
pattern

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

Tools

freyja
BSD-2-Clause

Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.