Skip to content

Latest commit

 

History

History

1.3.9

Folders and files

NameName
Last commit message
Last commit date

parent directory

..
 
 
 
 

freyja container

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.

Example Usage

# 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]