antismash

Description¶

antiSMASH allows the rapid genome-wide identification, annotation and analysis | of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.

Installation¶

ebi-metagenomics/antismash

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install antismash

Tools¶

antismash¶

antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell

Input¶

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	-
`contigs`	file	FASTA file containing the contigs genes originate from	`*.{fa,fasta}`
`genes`	file	GFF file containing the genes to be annotated by antiSMASH	`*.gff`
`gbk_input`	file	GenBank file to be annotated by antiSMASH	`*.ggk`
`antismash_db`	directory	antiSMASH database	-
`db_version`	string	antiSMASH database version string	-

Output¶

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	-
`gbk`	file	GENBANK output file from antiSMASH	`*.gbk`
`json`	file	JSON output file from antiSMASH	`*.json`
`results_tarball`	file	Compressed output result directory from antiSMASH	`*.tar.gz`
`versions`	file	File containing software versions	`versions.yml`