Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

kraken_report (file)

TSV file with six columns coming from kraken2 output

*.{tsv}

database (file)

Directory containing the kraken2/Bracken files for analysis

*

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

reports (file)

TSV output report of the re-estimated abundances

*.{tsv}

txt (file)

TXT file of bracken corrected results of Kraken2 report output

*.txt
included in
taxprofiler
author
Github user Midnighter
get in touch
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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