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freyja container

Main tool & documentation: freyja

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.

Additional tools

  • biopython 1.81
  • ivar 1.4.2
  • mafft 7.520
  • matplotlib-base 3.7.1
  • pandas 2.0.2
  • samtools 1.17
  • scipy 1.10.1
  • seaborn 0.12.2
  • ucsc-fatvcf 426
  • usher 0.6.2

freyja barcodes

This docker image was built on 2023-06-22 and the command freyja update is run as part of the build to retrieve the most up-to-date barcode file freyja/data/usher_barcodes.csv file from Freyja's GitHub repo. The barcode version included in this docker image is 06_22_2023-00-14 as reported by freyja demix --version

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]

Warning: freyja update does not work under all conditions. You may need to specify an output directory (freyja update --outdir /path/to/outdir) for which your user has write priveleges, such as a mounted volume.