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_deepbgc`

`${task.process}`
`:string`

The name of the process

`deepbgc`
`:string`

The name of the tool

`deepbgc info 2>&1 | sed '6!d;s/.= version //;s/ .//'`
`:eval`

The expression to obtain the version of the tool

`versions_prodigal`

`${task.process}`
`:string`

The name of the process

`prodigal`
`:string`

The name of the tool

`prodigal -v 2>&1 | sed '2!d;s/Prodigal V//;s/:.*//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`deepbgc`
`:string`

The name of the tool

`deepbgc info 2>&1 | sed '6!d;s/.= version //;s/ .//'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`prodigal`
`:string`

The name of the tool

`prodigal -v 2>&1 | sed '2!d;s/Prodigal V//;s/:.*//'`
`:eval`

The expression to obtain the version of the tool

Tools

deepbgc
MIT

DeepBGC - Biosynthetic Gene Cluster detection and classification

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