Description

Classify FASTQ files against ganon database

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fastqs (file)

Single or paired FASTQ files, optionally gzipped

*.{fq,fq.gz,fastq,fastq.gz}

dbs (file)

Ganon database files from build or build-custom

*.{ibf,tax}

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

tre (file)

Full ganon report file

*.tre

report (file)

Plain ganon report file with only targets with match

*.rep

lca (file)

Information about the lowest common ancestor match of a given read

*.lca

all (file)

Information of all matches to a given read

*.all

unc (file)

List of all reads without a hit

*.unc

log (file)

Text file containing console output from ganon classify

*.log
included in
taxprofiler
author
Github user jfy133
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Tools

ganon
MIT License

ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently

github.com/pirovc/ganon 10.1093/bioinformatics/btaa458