Description

Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth.

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

depths:file

File containing depth of the variants

*.depth.tsv

repeats:integer

Number of bootstrap repeats to perform

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

lineages

meta:map

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

]

*lineages.csv:file

a csv file that includes the lineages present and their corresponding abundances

*lineages.csv

summarized

meta:map

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

]

*summarized.csv:file

a csv file that includes the lineages present but summarized by constellation and their corresponding abundances

*summarized.csv

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.