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
reports
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.{tsv}
bracken_report:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.{tsv}
txt
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.txt
bracken_kraken_style_report:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.txt
versions
versions.yml:file
File containing software versions
versions.yml
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.
