Main tool : freyja
Full documentation: https://github.com/andersen-lab/Freyja/blob/main/README.md
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.
# run freyja variants to call variants from an aligned SC2 bam file
freyja variants [bamfile] --variants [variant outfile name] --depths [depths outfile name] --ref [reference.fa]
# run freyja demix to identify lineages based on called variants
freyja demix [variants-file] [depth-file] --output [output-file]