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:false ]

variants:file

File containing identified variants in a gff-like format

*.variants.tsv

depths:file

File containing depth of the variants

*.depth.tsv

barcodes:file

File containing lineage defining barcodes

*barcodes.csv

lineages_meta:file

File containing lineage metadata that correspond to barcodes

*lineages.json

Output

name:type
description
pattern

demix

meta:map

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

*.tsv:file

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

*.demix.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

freyja
BSD-2-Clause

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