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.
- biopython 1.81
- ivar 1.4.2
- mafft 7.520
- matplotlib-base 3.7.2
- pandas 2.0.3
- samtools 1.17
- scipy 1.11.1
- seaborn 0.12.2
- ucsc-fatovcf 448
- usher 0.6.2
This docker image was built on 2023-11-14 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 11_14_2023-00-57 as reported by freyja demix --version
# 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.