modules/freyja_boot

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.

variantsfastadeconvolutionwastewaterbootstrapping

https://github.com/nf-core/modules/[...]/modules/nf-core/freyja/boot

Description

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`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`

File containing lineage metadata that correspond to barcodes

*lineages.json

Output

name:type

description

pattern

`lineages{:bash}`

`meta{:bash}`
`:map`

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

`*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’, single_end:false ]

`*summarized.csv{:bash}`
`:file`

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

*summarized.csv

`versions{:bash}`

`versions.yml{:bash}`
`: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.

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

modules/freyja_boot

Description

Input

`meta{:bash}`
`:map`

`variants{:bash}`
`:file`

`depths{:bash}`
`:file`

`repeats{:bash}`
`:integer`

`barcodes{:bash}`
`:file`

`lineages_meta{:bash}`
`:file`

Output

`lineages{:bash}`

`meta{:bash}`
`:map`

`*lineages.csv{:bash}`
`:file`

`summarized{:bash}`

`meta{:bash}`
`:map`

`*summarized.csv{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

freyja
BSD-2-Clause

included in

maintainer

get in touch

modules/freyja_boot

Description

Input

meta{:bash}:map

variants{:bash}:file

depths{:bash}:file

repeats{:bash}:integer

barcodes{:bash}:file

lineages_meta{:bash}:file

Output

lineages{:bash}

meta{:bash}:map

*lineages.csv{:bash}:file

summarized{:bash}

meta{:bash}:map

*summarized.csv{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

freyja BSD-2-Clause

included in

maintainer

get in touch

`meta{:bash}`
`:map`

`variants{:bash}`
`:file`

`depths{:bash}`
`:file`

`repeats{:bash}`
`:integer`

`barcodes{:bash}`
`:file`

`lineages_meta{:bash}`
`:file`

`lineages{:bash}`

`meta{:bash}`
`:map`

`*lineages.csv{:bash}`
`:file`

`summarized{:bash}`

`meta{:bash}`
`:map`

`*summarized.csv{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

freyja
BSD-2-Clause