Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
module spider Freyja to find out what environment modules are available for this application.
- HPC_FREYJA_DIR - installation directory
- HPC_FREYJA_BIN - executable directory