Discover our collection of 2 research tools and applications for epidemiology.
Found 2 of 2 tools
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.
LYVE version of the Snp Extraction Tool (SET), a method of using hqSNPs to create a phylogeny.