Description

Build ganon database using custom reference sequences.

Input

name:type
description
pattern

meta:map

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

input:file

List of input FASTA files, or a directory containing input FASTA files. Note you must supply —input-extension via ext.args if FASTA extensions do not end in the default fna.gz.

*.{fasta,fna,fa,fa,fasta.gz,fna.gz,fa.gz,fa.gz}

input_tsv:string

(Optional) Specify an TSV file containing the paths, and relevant metadata to the input FASTA files to use the --input-file option. The ‘file’ column should be just the file name of each FASTA file (so that it’s local to the working directory of the process). See ganon documentation for more more information on the other columns.

*tsv

taxonomy_files:file

Pre-downloaded taxonomy files of input sequences. See ganon docs for formats

genome_size_files:file

Pre-downloaded NCBI or GTDB genome size files of input sequences. See ganon docs for formats

{species_genome_size.txt.gz,*_metadata.tar.gz}

Output

name:type
description
pattern

db

meta:map

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

*.{hibf,ibf,tax}:file

ganon database files

*.{ibf,tax}

info

meta:map

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

*.info.tsv:file

Copy of target info generated. Can be used for updating database.

*info.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ganon
MIT

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

github.com/pirovc/ganon 10.1093/bioinformatics/btaa458
createtaxdb
Github user jfy133
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