Description

Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.

Input

name:type
description
pattern

meta{:bash}

:map

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

kraken_report{:bash}

:file

TSV file with six columns coming from kraken2 output

*.{tsv}

database{:bash}

:file

Directory containing the kraken2/Bracken files for analysis

*

Output

name:type
description
pattern

reports{:bash}

meta{:bash}

:map

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

*.{tsv}

bracken_report{:bash}

:map

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

*.{tsv}

txt{:bash}

meta{:bash}

:map

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

*.{tsv}

bracken_kraken_style_report{:bash}

:map

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

*.txt

versions_bracken{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

bracken{:bash}

:string

The tool name

bracken -v | cut -f2 -d"v"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

bracken{:bash}

:string

The tool name

bracken -v | cut -f2 -d"v"{:bash}

:eval

The expression to obtain the version of the tool

Tools

bracken
GPL v3

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

ccb.jhu.edu/software/bracken ccb.jhu.edu/software/bracken/index.shtml?t=manual https://github.com/jenniferlu717/Bracken 10.7717/peerj-cs.104
included in
rnaseqtaxprofilerviralmetagenome
maintainer
Github user Midnighter
get in touch
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