specify the relative abundance of each known haplotype
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
variants
:file
File containing identified variants in a gff-like format
*.variants.tsv
depths
File containing depth of the variants
*.depth.tsv
barcodes
File containing lineage defining barcodes
*barcodes.csv
lineages_meta
File containing lineage metadata that correspond to barcodes
*lineages.json
demix
*.tsv
a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation
*.demix.tsv
versions
versions.yml
File containing software versions
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
