dbcan
Description¶
CAZyme annotation of proteins
Keywords: substrate prediction, annotation, cazyme
Installation¶
ebi-metagenomics/dbcan/easysubstrate
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install dbcan
Tools¶
dbcan¶
Standalone version of dbCAN annotation tool for automated CAZyme annotation
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
- |
fasta |
file | A FASTA file containing query sequences, they can be proteins of contigs | *.{fasta,faa,fa,fna} |
meta2 |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
- |
gff |
file | GFF file containing protein annotation information for the fasta file, only used then clusters are specified | *.gff |
dbcan_db |
directory | dbCAN database | dbcan_db |
db_version |
string | The version of the dbCAN database | - |
mode |
string | Type of sequence input. protein=proteome; prok=prokaryote; meta=metagenome | - |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
overview_txt |
file | - | |
dbsub_output_tsv |
file | - | |
dbhmm_output_tsv |
file | - | |
diamond_output |
file | - | |
uniinput_faa |
file | - | |
cgc_gff |
file | - | |
cgc_standard_tsv |
file | - | |
substrate_prediction_tsv |
file | - | |
synteny_pdfs |
file | - | |
versions |
file | - |