Description

DeepBGC detects BGCs in bacterial and fungal genomes using deep learning.

Input

Name (Type)
Description
Pattern

meta (map)

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

genome (file)

FASTA/GenBank/Pfam CSV file

*.{fasta,fa,fna,gbk,csv}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

readme (file)

txt file containing description of output files

*.{txt}

log (file)

Log output of DeepBGC

*.{txt}

json (file)

AntiSMASH JSON file for sideloading

*.{json}

bgc_gbk (file)

Sequences and features of all detected BGCs in GenBank format

*.{bgc.gbk}

bgc_tsv (file)

Table of detected BGCs and their properties

*.{bgc.tsv}

full_gbk (file)

Fully annotated input sequence with proteins, Pfam domains (PFAM_domain features) and BGCs (cluster features)

*.{full.gbk}

pfam_tsv (file)

Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores

*.{pfam.tsv}

bgc_png (file)

Detected BGCs plotted by their nucleotide coordinates

*.{bgc.png}

pr_png (file)

Precision-Recall curve based on predicted per-Pfam BGC scores

*.{pr.png}

roc_png (file)

ROC curve based on predicted per-Pfam BGC scores

*.{roc.png}

score_png (file)

BGC detection scores of each Pfam domain in genomic order

*.{score.png}
included in
funcscan
authors
Github user louperelo Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

deepbgc
MIT

DeepBGC - Biosynthetic Gene Cluster detection and classification

github.com/Merck/deepbgc 10.1093/nar/gkz654