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{:bash}

:map

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

variants{:bash}

:file

File containing identified variants in a gff-like format

*.variants.tsv

depths{:bash}

:file

File containing depth of the variants

*.depth.tsv

repeats{:bash}

:integer

Number of bootstrap repeats to perform

barcodes{:bash}

:file

File containing lineage defining barcodes

*barcodes.csv

lineages_meta{:bash}

:file

Optional file containing lineage metadata that correspond to barcodes

*lineages.json

lineages_topology{:bash}

:file

Optional file containing lineage topology information that correspond to barcodes

*lineages.yml

Output

name:type
description
pattern

lineages{:bash}

meta{:bash}

:map

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

*lineages.csv{:bash}

:file

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

*lineages.csv

summarized{:bash}

meta{:bash}

:map

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

*summarized.csv{:bash}

:file

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

*summarized.csv

versions_freyja{:bash}

${task.process}{:bash}

:string

The name of the process

freyja{:bash}

:string

The name of the tool

freyja --version | sed 's/.* //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

freyja{:bash}

:string

The name of the tool

freyja --version | sed 's/.* //'{:bash}

:eval

The expression to obtain the version of the tool

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
included in
viralrecon
maintainer
Github user Joon-Klaps
get in touch
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