antismash
Description¶
antiSMASH allows the rapid genome-wide identification, annotation and analysis | of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
Keywords: bgc, biosynthetic gene cluster, antismash
Installation¶
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 |
People¶
Authors¶
Maintainers