modules/deepbgc_pipeline

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

BGCbiosynthetic gene clusterdeep learningneural networkrandom forestgenomesbacteriafungi

https://github.com/nf-core/modules/[...]/modules/nf-core/deepbgc/pipeline

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}

`db:directory`

Database path

Output

name:type

description

pattern

`readme`

`meta:map`

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

`${prefix}/README.txt:file`

txt file containing description of output files

*.{txt}

`log`

`meta:map`

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

`${prefix}/LOG.txt:file`

Log output of DeepBGC

*.{txt}

`json`

`meta:map`

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

`${prefix}/${prefix}.antismash.json:file`

AntiSMASH JSON file for sideloading

*.{json}

`bgc_gbk`

`meta:map`

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

`${prefix}/${prefix}.bgc.gbk:file`

Sequences and features of all detected BGCs in GenBank format

*.{bgc.gbk}

`bgc_tsv`

`meta:map`

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

`${prefix}/${prefix}.bgc.tsv:file`

Table of detected BGCs and their properties

*.{bgc.tsv}

`full_gbk`

`meta:map`

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

`${prefix}/${prefix}.full.gbk:file`

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

*.{full.gbk}

`pfam_tsv`

`meta:map`

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

`${prefix}/${prefix}.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`

`meta:map`

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

`${prefix}/evaluation/${prefix}.bgc.png:file`

Detected BGCs plotted by their nucleotide coordinates

*.{bgc.png}

`pr_png`

`meta:map`

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

`${prefix}/evaluation/${prefix}.pr.png:file`

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

*.{pr.png}

`roc_png`

`meta:map`

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

`${prefix}/evaluation/${prefix}.roc.png:file`

ROC curve based on predicted per-Pfam BGC scores

*.{roc.png}

`score_png`

`meta:map`

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

`${prefix}/evaluation/${prefix}.score.png:file`

BGC detection scores of each Pfam domain in genomic order

*.{score.png}

`versions`

`versions.yml: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