Description

Build centrifuge database for taxonomic profiling

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

Fasta file containing sequences to be used in centrifuge database.

*.{fasta,fna}

conversion_table (file)

A tab-separated file with sequence ID to taxonomy ID mapping

*.{map}

taxonomy_tree (file)

A \t|\t-separated file mapping taxonomy. Typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents

*.{dmp}

name_table (file)

A ’|‘-separated file mapping taxonomy IDs to a name. Typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name

*.{dmp}

size_table (file)

Optional list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.

*

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

cf (file)

Index files for the centrifuge database

*.{cf}
included in
createtaxdb
maintainers
Github user sarah-buddle
Github user jfy133
get in touch
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