Description

Extends a Kraken2 database to be compatible with Bracken

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

k2d{:bash}

:file

Kraken2 k2d binary database files

*.k2d

map{:bash}

:file

Kraken2 k2d binary database taxonomy to sequencing mapping file

*.map

library{:bash}

:file

Kraken2 masked FASTA files used to build the database

*.fasta

taxonomy{:bash}

:file

Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files

*.{dmp,accession2taxid}

Output

name:type
description
pattern

db{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

bracken-database/{:bash}

:directory

Directory contains the database that can be used to perform taxonomic classification

IMPORTANT: this output directory will be hardcoded as ‘bracken-database/’ inside the module to prevent issues of containers following symlinks in symlinks.

To give a user the option to provide custom name for the database directory within a pipeline, you should customise this name using during pipeline output publication via the pipeline’s publishDir or workflow output customisation options.

bracken-database/

db_separated{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

bracken-database/database*{:bash}

:file

Bracken kmer distribution files

database*

bracken-database/*k2d{:bash}

:file

Kraken2 k2d binary database files

*.k2d

bracken-database/*map{:bash}

:file

Kraken2 k2d binary database taxonomy to sequencing mapping file

*.map

bracken-database/library/added/*{:bash}

:file

Kraken2 masked FASTA files used to build the database

*.fasta

bracken-database/taxonomy/*{:bash}

:file

Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files

*.{dmp,accession2taxid}

versions{:bash}

versions.yml{:bash}

: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.

ccb.jhu.edu/software/bracken https://github.com/jenniferlu717/Bracken/ 10.7717/peerj-cs.104
included in
createtaxdb
maintainer
Github user jfy133
get in touch
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