Description

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

sequence_input (file)

nucleotide sequence file (annotated)

*.{gbk, gb, gbff, genbank, embl, fasta, fna}

databases (directory)

Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory
”data/databases”)

*/

antismash_dir (directory)

A local copy of an AntiSMASH installation folder. This is required when running with
docker and singularity (not required for conda), due to attempted ‘modifications’ of
files during database checks in the installation directory, something that cannot
be done in immutable docker/singularity containers. Therefore, a local installation
directory needs to be mounted (including all modified files from the downloading step)
to the container as a workaround.

*/

gff (file)

Annotations in GFF3 format (only if sequence_input is in FASTA format)

*.gff

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

clusterblast_file (file)

Output of ClusterBlast algorithm

clusterblast/*_c*.txt

html_accessory_files (directory)

Accessory files for the HTML output

{css/,images/,js/}

knownclusterblast_html (file)

Tables with MIBiG hits in HTML format

knownclusterblast/region*/ctg*.html

knownclusterblast_dir (directory)

Directory with MIBiG hits

knownclusterblast/

knownclusterblast_txt (file)

Tables with MIBiG hits

knownclusterblast/*_c*.txt

svg_files_clusterblast (file)

SVG images showing the % identity of the aligned hits against their queries

svg/clusterblast*.svg

svg_files_knownclusterblast (file)

SVG images showing the % identity of the aligned hits against their queries

svg/knownclusterblast*.svg

gbk_input (file)

Nucleotide sequence and annotations in GenBank format; converted from input file

*.gbk

json_results (file)

Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)

*.json

log (file)

Contains all the logging output that antiSMASH produced during its run

*.log

zip (file)

Contains a compressed version of the output folder in zip format

*.zip

gbk_results (file)

Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit

*region*.gbk

clusterblastoutput (file)

Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm

clusterblastoutput.txt

html (file)

Graphical web view of results in HTML format

knownclusterblastoutput (file)

Raw BLAST output of known clusters of the MIBiG database

knownclusterblastoutput.txt

json_sideloading (file)

Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation “Annotation sideloading”)

regions.js

Tools

antismashlite
AGPL v3

antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell