Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

genome{:bash}

:file

FASTA/GenBank/Pfam CSV file

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

db{:bash}

:directory

Database path

Output

name:type
description
pattern

readme{:bash}

meta{:bash}

:map

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

${prefix}/README.txt{:bash}

:file

txt file containing description of output files

*.{txt}

log{:bash}

meta{:bash}

:map

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

${prefix}/LOG.txt{:bash}

:file

Log output of DeepBGC

*.{txt}

json{:bash}

meta{:bash}

:map

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

${prefix}/${prefix}.antismash.json{:bash}

:file

AntiSMASH JSON file for sideloading

*.{json}

bgc_gbk{:bash}

meta{:bash}

:map

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

${prefix}/${prefix}.bgc.gbk{:bash}

:file

Sequences and features of all detected BGCs in GenBank format

*.{bgc.gbk}

bgc_tsv{:bash}

meta{:bash}

:map

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

${prefix}/${prefix}.bgc.tsv{:bash}

:file

Table of detected BGCs and their properties

*.{bgc.tsv}

full_gbk{:bash}

meta{:bash}

:map

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

${prefix}/${prefix}.full.gbk{:bash}

:file

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

*.{full.gbk}

pfam_tsv{:bash}

meta{:bash}

:map

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

${prefix}/${prefix}.pfam.tsv{:bash}

:file

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

*.{pfam.tsv}

bgc_png{:bash}

meta{:bash}

:map

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

${prefix}/evaluation/${prefix}.bgc.png{:bash}

:file

Detected BGCs plotted by their nucleotide coordinates

*.{bgc.png}

pr_png{:bash}

meta{:bash}

:map

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

${prefix}/evaluation/${prefix}.pr.png{:bash}

:file

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

*.{pr.png}

roc_png{:bash}

meta{:bash}

:map

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

${prefix}/evaluation/${prefix}.roc.png{:bash}

:file

ROC curve based on predicted per-Pfam BGC scores

*.{roc.png}

score_png{:bash}

meta{:bash}

:map

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

${prefix}/evaluation/${prefix}.score.png{:bash}

:file

BGC detection scores of each Pfam domain in genomic order

*.{score.png}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

deepbgc
MIT

DeepBGC - Biosynthetic Gene Cluster detection and classification

github.com/Merck/deepbgc 10.1093/nar/gkz654
included in
funcscan
maintainers
Github user louperelo
Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub