Freyja

Recovers relative lineage abundances from mixed SARS-CoV-2 samples

https://github.com/andersen-lab/Freyja

Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset and uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree to solve the constrained (unit sum, non-negative) de-mixing problem.

File search patterns

freyja:
  contents: "summarized\t["
  fn: "*.tsv"
  num_lines: 6