Description

specify the relative abundance of each known haplotype

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

variants (file)

File containing identified variants in a gff-like format

*.variants.tsv

meta2 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

depths (file)

File containing depth of the variants

*.depth.tsv

meta3 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

barcodes (file)

File containing lineage defining barcodes

*barcodes.csv

meta4 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

lineages_meta (file)

File containing lineage metadata that correspond to barcodes

*lineages.json

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

demix (file)

a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation

*.demix.tsv

versions (file)

File containing software versions

versions.yml
author
Github user Joon-Klaps
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Tools

freyja
BSD-2-Clause

Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.

github.com/andersen-lab/Freyja github.com/andersen-lab/Freyja/wiki https://github.com/andersen-lab/Freyja 10.1038/s41586-022-05049-6