bgc_quast_ppl

A Nextflow pipeline that predicts biosynthetic gene clusters (BGCs) in genome assemblies and compares the predictions in one report.

1. Introduction

bgc_quast_ppl takes one or more genome assemblies and finds the BGCs in them with three prediction tools: antiSMASH, DeepBGC and GECCO. It then passes the results to bgc-quast, which counts, measures and compares the predicted BGCs and writes one report per comparison.

BGC-QUAST is a quality assessment tool for BGC prediction tools, made by the Gurevich lab. This pipeline runs all the steps before bgc-quast for you, so you only need your genome files.

You can compare BGCs in three ways:

across samples - one tool, many genomes
across tools - one genome, three tools
against a reference - draft genomes against one high-quality genome

An optional step runs BiG-SCAPE, which groups similar BGCs into gene cluster families (GCFs) and adds family numbers to the reports.

The pipeline reuses parts of nf-core/funcscan 3.0.0 for input preparation, gene annotation and BGC prediction.

2. Pipeline summary

bgc_quast_ppl pipeline diagram

Unzip the input genomes if they are compressed.
Remove short contigs with SeqKit (default: shorter than 3,000 bp).
Find genes with Pyrodigal. Each genome is annotated once, and the same annotation goes to all three prediction tools.
Predict BGCs with antiSMASH, DeepBGC and GECCO.
Compare-to-reference mode only: align each draft genome to the reference with QUAST.
Optional, compare-samples mode only: group BGCs into families with BiG-SCAPE.
Compare the predictions and write the reports with bgc-quast.

3. Quick start

export NXF_VER=25.10.5

nextflow run . \
  -profile docker \
  --input samplesheet.csv \
  --outdir results \
  --bgc_antismash_db /absolute/path/to/antismash_db_v8 \
  --bgc_deepbgc_db /absolute/path/to/deepbgc_db \
  --max_cpus 4 \
  --max_memory 24.GB

This runs the default mode, compare-samples. Read sections 4 to 7 before your first run.

4. Requirements

Requirement	Details
Nextflow	Version 25.10.x only. Tested with 25.10.4 and 25.10.5. Other versions stop at the start. Version 26.01 and newer does not work.
Docker	Must be installed and running before you start. Every tool except bgc-quast runs inside a Docker container.
Python 3.9 to 3.13	With `pandas`, `biopython` and `pyyaml`. bgc-quast runs directly on your machine, not in a container. See Important notes.
antiSMASH database	Version 8. See Databases.
DeepBGC database	See Databases.
Pfam-A.hmm	Only if you turn on BiG-SCAPE. It can be downloaded for you.
Disk space	Several GB for the databases, plus space for the work folder.

GECCO needs no database. Its model is inside its container.

5. Installation

Get the pipeline. Use one of these two ways.

With HTTPS (works for everyone):

git clone https://github.com/Seg0fieD/bgc_quast_ppl.git
cd bgc_quast_ppl

With SSH (needs an SSH key added to your GitHub account):

git clone git@github.com:Seg0fieD/bgc_quast_ppl.git
cd bgc_quast_ppl

Fix the Nextflow version. Do this once in every new terminal, before any nextflow command:

export NXF_VER=25.10.5

Set up the Python packages bgc-quast needs, for example with conda:

conda env create -f bin/bgc-quast/environment.yml
conda activate bgc-quast

Then install Nextflow in the same environment, or make sure the nextflow command can find this Python.

6. Databases

antiSMASH and DeepBGC need their databases on disk before the run. The pipeline stops at the start if a path is missing.

Database	Parameter	How to get it
antiSMASH v8	`--bgc_antismash_db`	Follow the antiSMASH download guide. The database must match antiSMASH 8.
DeepBGC	`--bgc_deepbgc_db`	Run `deepbgc download`. See the DeepBGC page.
Pfam-A (for BiG-SCAPE)	`--bgc_bigscape_pfam`	Optional. If you leave it out, the pipeline downloads Pfam 38.2 for you.

Important

Always give database paths as absolute paths (starting with /).

Pfam in detail. --bgc_bigscape_pfam must point to the Pfam-A.hmm file, not its folder. The four index files .h3f, .h3i, .h3m and .h3p must sit next to it. If they are missing, run this once:

hmmpress Pfam-A.hmm

If you do not give a Pfam file, the pipeline downloads about 400 MB and needs about 4 GB of free disk. Add --save_db to keep the download in <outdir>/databases/pfam/, so you can reuse it next time.

7. The samplesheet

The input is a CSV file with a header row. Pass it with --input.

Column	Required	Meaning
`sample`	Yes	A unique name for the genome. No spaces.
`fasta`	Yes	Path to the genome. Allowed endings: `.fasta`, `.fna`, `.fa`, `.fas`, each with or without `.gz`.
`type`	Only in compare-to-reference	`q` for a query genome, `r` for the reference. Upper or lower case both work.

The first two columns must be sample and fasta, in that order.

For compare-samples and compare-tools:

sample,fasta
assembly_10,data/assembly_10.fasta.gz
assembly_20,data/assembly_20.fasta.gz

For compare-to-reference: add the type column. Use exactly one reference row (r) and one or more query rows (q).

sample,fasta,type
assembly_10,data/assembly_10.fasta.gz,q
assembly_20,data/assembly_20.fasta.gz,q
reference,data/reference.fasta.gz,r

The name of the reference row is used as the reference label in the report.

Rules to keep in mind:

Every sample name must be unique.
If you leave a sample name empty, the pipeline makes one from the file name and tells you.
With BiG-SCAPE on, a sample name must not contain .region or _cluster_. The pipeline uses these to match files and stops if it finds them.
Relative paths are read from the folder you start the pipeline in.

A ready-made example is in example_test_data/samplesheet.csv.

8. Comparison modes

Choose the mode with --bgc_quast_mode. Each run uses one mode.

Mode	What it compares	You get	Use it to answer
`compare-samples` (default)	All samples, one tool at a time	One report per tool	"How do my genomes differ from each other?"
`compare-tools`	The three tools, one sample at a time	One report per sample	"For this genome, how do antiSMASH, DeepBGC and GECCO differ?"
`compare-to-reference`	Each draft genome against one reference	One report per tool	"How many of the reference BGCs did my drafts recover?"

What each mode reports:

All modes: number of BGCs, mean BGC length, total BGC span and mean number of genes per BGC. Each is also split by product type and by completeness. A BGC is complete when it does not touch a contig edge.
compare-tools: which BGCs each tool finds alone and which are shared, with Venn diagrams. It also writes a combined table and GenBank file of all predicted BGCs.
compare-to-reference: how many reference BGCs are fully recovered, partly recovered or missed in each draft. QUAST runs for you.
compare-samples with BiG-SCAPE: number of gene cluster families, families shared between samples, and a Venn diagram.

For the full list of metrics, see the bgc-quast metrics page.

Note

auto is listed as a mode but is not available yet. Choosing it stops the run and an error is thrown at the start-up.

9. Running the pipeline

Start every run from inside the bgc_quast_ppl folder. Replace the paths with your own.

Compare samples (default)

nextflow run . \
  -profile docker \
  --input samplesheet.csv \
  --outdir results \
  --bgc_quast_mode compare-samples \
  --bgc_antismash_db /absolute/path/to/antismash_db_v8 \
  --bgc_deepbgc_db /absolute/path/to/deepbgc_db \
  --max_cpus 2 \
  --max_memory 16.GB

Compare tools

The same command with a different mode:

  --bgc_quast_mode compare-tools \

Compare to reference

Use a samplesheet with a type column and one reference row:

nextflow run . \
  -profile docker \
  --input samplesheet_ref.csv \
  --outdir results \
  --bgc_quast_mode compare-to-reference \
  --bgc_antismash_db /absolute/path/to/antismash_db_v8 \
  --bgc_deepbgc_db /absolute/path/to/deepbgc_db \
  --max_cpus 2 \
  --max_memory 16.GB

Compare samples with gene cluster families (BiG-SCAPE)

nextflow run . \
  -profile docker \
  --input samplesheet.csv \
  --outdir results \
  --bgc_quast_mode compare-samples \
  --run_bigscape \
  --bgc_bigscape_pfam /absolute/path/to/Pfam-A.hmm \
  --bgc_antismash_db /absolute/path/to/antismash_db_v8 \
  --bgc_deepbgc_db /absolute/path/to/deepbgc_db \
  --max_cpus 2 \
  --max_memory 16.GB

See all parameters in the terminal

nextflow run . --help

Tip

Give parameters on the command line or in a file with -params-file. Do not put parameters in a custom config file (-c). Use config files only for settings such as resources.

10. Parameters

All parameters start with two dashes (--). A parameter without a value, such as --run_bigscape, turns an option on. Defaults are shown in the tables.

10.1 Input and output

Parameter	Default	What it does
`--input`	-	Path to your samplesheet. Required.
`--outdir`	-	Folder for the results. Required.
`--email`	-	Send a short summary email when the run ends.

10.2 Comparison with bgc-quast

Parameter	Default	What it does
`--bgc_quast_mode`	`compare-samples`	Which comparison to run: `compare-samples`, `compare-tools` or `compare-to-reference`. See Comparison modes.
`--bgc_quast_edge_distance`	`100`	A BGC closer than this many bp to a contig edge is labelled incomplete. This only labels BGCs. It does not remove any.
`--bgc_quast_min_bgc_length`	`0`	Leave out BGCs shorter than this many bp. `0` keeps all BGCs.
`--bgc_quast_merge_distance`	`0`	Join two BGCs into one when the gap between them is this many bp or less. `0` turns joining off.
`--bgc_quast_overlap_fraction`	`0.9`	How much two BGCs must overlap to count as the same BGC. A number between 0 and 1. Used in compare-tools only.
`--bgc_quast_quastdir`	-	Use your own finished QUAST output folder instead of running QUAST. Compare-to-reference only.
`--bgc_quast_debug`	`false`	Keep bgc-quast's temporary files, and print the full error message if a step fails.

10.3 BGC prediction: general

Parameter	Default	What it does
`--bgc_mincontiglength`	`3000`	Contigs shorter than this many bp are removed before prediction. The same value is used for QUAST.
`--bgc_savefilteredcontigs`	`false`	Save the length-filtered contigs to `<outdir>/bgc/seqkit/`.
`--bgc_skip_antismash`	`false`	Do not run antiSMASH.
`--bgc_skip_deepbgc`	`false`	Do not run DeepBGC.
`--bgc_skip_gecco`	`false`	Do not run GECCO.
`--run_bgc_screening`	`true`	Leave this on. Turning it off skips BGC prediction and all comparisons.

10.4 antiSMASH

antiSMASH runs in minimal mode by default. Minimal mode finds the BGCs and skips the extra analyses, so it is much faster.

Parameter	Default	What it does
`--bgc_antismash_db`	-	Path to the antiSMASH v8 database folder. Required unless antiSMASH is skipped.
`--bgc_antismash_full`	`false`	Run the full analysis instead of minimal mode.
`--bgc_antismash_minimal`	`false`	Run minimal mode. This is already the default, so you do not need it. Do not use it together with `--bgc_antismash_full`.
`--bgc_antismash_taxon`	`bacteria`	Type of organism: `bacteria` or `fungi`.
`--bgc_antismash_hmmdetectionstrictness`	`relaxed`	How strict BGC detection is: `strict`, `relaxed` or `loose`. `loose` finds more, less certain BGCs.
`--bgc_antismash_contigminlength`	`3000`	antiSMASH skips contigs shorter than this many bp.
`--bgc_antismash_cbgeneral`	`false`	Compare BGCs with a database of antiSMASH-predicted BGCs (ClusterBlast).
`--bgc_antismash_cbknownclusters`	`false`	Compare BGCs with known BGCs from MIBiG (KnownClusterBlast).
`--bgc_antismash_cbsubclusters`	`false`	Compare BGCs with known sub-clusters (SubClusterBlast).
`--bgc_antismash_ccmibig`	`false`	Compare BGCs with MIBiG using ClusterCompare.
`--bgc_antismash_smcogtrees`	`false`	Build family trees for the BGC genes.
`--bgc_antismash_pfam2go`	`false`	Link protein domains to Gene Ontology terms.
`--bgc_antismash_rre`	`false`	Search RiPP clusters for RRE elements.
`--bgc_antismash_tfbs`	`false`	Search for transcription factor binding sites.

The extra analyses add time and output files. They do not change which BGCs are found, so they do not change the bgc-quast reports.

10.5 DeepBGC

Parameter	Default	What it does
`--bgc_deepbgc_db`	-	Path to the DeepBGC database folder. Required unless DeepBGC is skipped.
`--bgc_deepbgc_score`	`0.5`	Lowest score a region needs to be called a BGC. Higher means fewer, more certain BGCs.
`--bgc_deepbgc_classifierscore`	`0.5`	Lowest score needed to give a BGC a product class.
`--bgc_deepbgc_minnucl`	`1`	Smallest BGC length to report, in bp.
`--bgc_deepbgc_minproteins`	`1`	Smallest number of proteins a BGC must have.
`--bgc_deepbgc_mindomains`	`1`	Smallest number of protein domains a BGC must have.
`--bgc_deepbgc_minbiodomains`	`0`	Smallest number of known biosynthetic domains a BGC must have.
`--bgc_deepbgc_mergemaxproteingap`	`0`	Join BGCs that are this many proteins apart or closer.
`--bgc_deepbgc_mergemaxnuclgap`	`0`	Join BGCs that are this many bp apart or closer.
`--bgc_deepbgc_prodigalsinglemode`	`false`	Run DeepBGC's own gene finder in single-genome mode. The pipeline already gives DeepBGC the genes, so this usually has no effect.

10.6 GECCO

Parameter	Default	What it does
`--bgc_gecco_threshold`	`0.8`	Lowest probability a gene needs to be part of a BGC. Lower gives more and longer BGCs, but less accurate ones.
`--bgc_gecco_cds`	`3`	Smallest number of genes a BGC must have.
`--bgc_gecco_pfilter`	`1e-9`	p-value cut-off for protein domains.
`--bgc_gecco_edgedistance`	`0`	Smallest number of genes between a BGC and the contig edge.
`--bgc_gecco_mask`	`false`	Stop genes from running across unknown bases (`N`).

10.7 BiG-SCAPE (gene cluster families)

BiG-SCAPE is off by default and runs only in compare-samples mode. With any other mode, --run_bigscape stops the run at start-up with an error. BiG-SCAPE runs once for each prediction tool that is switched on, over all samples together.

Parameter	Default	What it does
`--run_bigscape`	`false`	Turn BiG-SCAPE on.
`--bgc_bigscape_pfam`	-	Path to your `Pfam-A.hmm` file. Leave it out to download Pfam automatically.
`--bgc_bigscape_pfam_url`	Pfam 38.2	Where to download Pfam from. Only used when no Pfam file is given.
`--bgc_bigscape_cutoffs`	`0.3,0.5,0.7`	Family cut-offs to compute, separated by commas. A lower cut-off makes smaller, tighter families. You can switch between them in the HTML report.
`--bgc_bigscape_cutoff`	`0.3`	The cut-off shown in the report table. It must be one of `--bgc_bigscape_cutoffs`.
`--bgc_bigscape_dir`	-	Reuse BiG-SCAPE results from an earlier run. Point it at that run's `bgc_quast/bigscape/` folder. Tools found there are not run again.
`--bgc_bigscape_classify`	`none`	How BiG-SCAPE sorts BGCs into bins before grouping. Fixed to `none`, because the report reads the single mixed bin.

10.8 Gene annotation

The pipeline finds genes with Pyrodigal before prediction.

Parameter	Default	What it does
`--annotation_tool`	`pyrodigal`	Gene finder. `pyrodigal` is the only supported choice.
`--save_annotations`	`false`	Save the annotation files to `<outdir>/annotation/`.

Pyrodigal options

Parameter	Default	What it does
`--annotation_pyrodigal_singlemode`	`false`	Use single-genome mode instead of metagenome mode. Single mode needs contigs of at least 20,000 bp.
`--annotation_pyrodigal_closed`	`false`	Do not allow genes to run off the contig ends.
`--annotation_pyrodigal_transtable`	`11`	Genetic code table. 11 is for bacteria and archaea.
`--annotation_pyrodigal_forcenonsd`	`false`	Do a full motif scan instead of the Shine-Dalgarno finder.
`--annotation_pyrodigal_usespecialstopcharacter`	`false`	Add `*` at the end of each protein sequence.

10.9 Resources

Parameter	Default	What it does
`--max_cpus`	`2`	Most CPUs any one step may use.
`--max_memory`	`8.GB`	Most memory any one step may use.
`--max_time`	`24.h`	Longest time any one step may run.

Important

The defaults are low. Every step is held to 2 CPUs and 8 GB unless you raise them. Set these to fit your computer, for example --max_cpus 4 --max_memory 32.GB.

10.10 Other options

Parameter	Default	What it does
`--save_db`	`false`	Keep databases the pipeline downloads (Pfam) in `<outdir>/databases/`.
`--publish_dir_mode`	`copy`	How results are placed in `--outdir`: `copy`, `symlink`, `link`, `move` and others.
`--email_on_fail`	-	Send an email only when the run fails.
`--monochrome_logs`	`false`	Print messages without colour.
`--validate_params`	`true`	Check all parameters before the run starts. Leave this on.

11. Output

All results go into the folder you gave with --outdir.

results/
|-- bgc/                          raw output of each prediction tool
|   |-- antismash/<sample>/
|   |-- deepbgc/<sample>/
|   |-- gecco/<sample>/
|   `-- seqkit/                   only with --bgc_savefilteredcontigs
|-- bgc_quast/
|   |-- compare_samples/          compare-samples mode
|   |   |-- antiSMASH/
|   |   |-- DeepBGC/
|   |   `-- GECCO/
|   |-- compare_tools/            compare-tools mode
|   |   `-- <sample>/
|   |-- compare_to_reference/     compare-to-reference mode
|   |   |-- antiSMASH/
|   |   |-- DeepBGC/
|   |   `-- GECCO/
|   |-- quast/                    compare-to-reference mode only
|   `-- bigscape/                 only with --run_bigscape
|       |-- antismash/
|       |-- deepbgc/
|       `-- gecco/
|-- annotation/                   only with --save_annotations
|-- databases/                    only with --save_db
`-- pipeline_info/                run reports, timeline and software versions

Only the folder of the mode you ran is created. A skipped tool has no folder.

Files in each bgc-quast report folder:

File	Contents
`report.html`	The interactive report. Open it in a web browser. Start here.
`report.tsv`	The same numbers as a table.
`report.txt`	The same numbers as plain text.
`bgc-quast.log`	The log of the bgc-quast run.

In compare-tools mode, each sample folder also has:

File	Contents
`all_tools.bgcs.tsv`	Every BGC from every tool, sorted by position.
`all_tools.bgcs.overlaps.tsv`	BGCs grouped where they overlap.
`all_tools.bgcs.overlaps.html`	The same groups as a table you can search and filter.
`all_tools.bgcs.gbk`	The genome with the BGCs of all tools marked on it.

Each BiG-SCAPE folder holds BiG-SCAPE's own results, including its interactive index.html page.

12. Important notes

Samples without BGCs are left out of that tool's report, and a note at the end of the run names them. This note appears only when the run succeeds. An empty reference gives no report for that tool.
Short contigs below --bgc_mincontiglength are removed. A sample with none left is skipped, with a warning at the end of the run.
One annotation for all tools. All three tools get the same Pyrodigal genes, so tool differences come from BGC finding, not gene finding.
Gene counts come from Pyrodigal. Compare them only within one run.
bgc-quast runs outside Docker. Your Python needs pandas, biopython and pyyaml (see Installation).
Tested setup: -profile docker on Ubuntu 24.04 and macOS. Other profiles are untested.
GECCO in BiG-SCAPE uses BiG-SCAPE's experimental --force-gbk option.
Family numbers are reproducible. The same input gives the same families. To reuse one result, pass it with --bgc_bigscape_dir.
Pfam is pinned to release 38.2, because other releases can change the families.
Compare family numbers at the same cut-off only.
Pre-annotated genomes (gbk and protein columns, given together) are accepted but untested.

13. Resuming a run

If a run stops, add -resume to the same command. Finished steps are reused and only the rest runs.

nextflow run . -profile docker --input samplesheet.csv --outdir results -resume

Warning

Keep the same --outdir.
Do not change database options on a -resume.
Changing only --max_cpus or --max_memory does not make a finished step run again.
If you edit files inside bin/bgc-quast/, run without -resume. Nextflow does not notice those edits and would reuse the old report.

14. Troubleshooting

Problem	What to do
`nextflow: command not found`	Install Nextflow, then run `export NXF_VER=25.10.5`.
Errors about the Nextflow version	Run `export NXF_VER=25.10.5` in this terminal. Only 25.10.x works; 26.01 and newer fail while reading the config.
"Docker does not seem to be running"	Start Docker and run the command again.
"Cannot start. Please fix: ..."	The pipeline checked your input and settings before starting. Fix each listed problem and run again.
antiSMASH or DeepBGC database errors	Check that the paths are absolute and correct, and that the antiSMASH database is version 8.
"Pfam is not pressed"	Run `hmmpress Pfam-A.hmm` once.
bgc-quast fails with a Python import error	Install `pandas`, `biopython` and `pyyaml` in the Python that runs Nextflow.
Red "did NOT complete successfully" box, but no error	The run ended but produced no comparison. Usually every contig was shorter than `--bgc_mincontiglength`, or no tool found any BGC. Check your genomes.
A step failed and you need more detail	Run again with `--bgc_quast_debug` to print the full error message. The failed step's folder in `work/` also has a `.command.err` file with the whole error.
The run seems stuck	Check `docker ps` and the step's folder in `work/`. If the step already finished, stop the run and start it again with `-resume`.

15. Citations

If you use bgc_quast_ppl, please cite this repository and the version you used, for example:

bgc_quast_ppl, version 2.1.0. https://github.com/Seg0fieD/bgc_quast_ppl

Results can change between versions. See VERSION_LOG.md for what changed in each one.

Please also cite the tools it runs:

bgc-quast - Kushnareva, Tupikina et al., bioRxiv 2026. Preprint, GitHub
antiSMASH - antiSMASH
DeepBGC - DeepBGC
GECCO - GECCO
BiG-SCAPE - BiG-SCAPE
QUAST - QUAST
Pyrodigal - Pyrodigal
SeqKit - SeqKit
nf-core/funcscan - docs 3.0.0, GitHub 3.0.0, doi:10.5281/zenodo.7643099
nf-core - Ewels et al., Nature Biotechnology 2020. doi:10.1038/s41587-020-0439-x
Nextflow - nextflow.io

Questions and bug reports: GitHub Issues.

Name		Name	Last commit message	Last commit date
assets		assets
bin/bgc-quast		bin/bgc-quast
conf		conf
docs/images		docs/images
example_pipeline_output/bgc_quast		example_pipeline_output/bgc_quast
example_test_data		example_test_data
modules		modules
subworkflows		subworkflows
workflows		workflows
.gitignore		.gitignore
.nf-core.yml		.nf-core.yml
README.md		README.md
VERSION_LOG.md		VERSION_LOG.md
main.nf		main.nf
modules.json		modules.json
nextflow.config		nextflow.config
nextflow_schema.json		nextflow_schema.json

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bgc_quast_ppl

Contents

1. Introduction

2. Pipeline summary

3. Quick start

4. Requirements

5. Installation

6. Databases

7. The samplesheet

8. Comparison modes

9. Running the pipeline

Compare samples (default)

Compare tools

Compare to reference

Compare samples with gene cluster families (BiG-SCAPE)

See all parameters in the terminal

10. Parameters

10.1 Input and output

10.2 Comparison with bgc-quast

10.3 BGC prediction: general

10.4 antiSMASH

10.5 DeepBGC

10.6 GECCO

10.7 BiG-SCAPE (gene cluster families)

10.8 Gene annotation

10.9 Resources

10.10 Other options

11. Output

12. Important notes

13. Resuming a run

14. Troubleshooting

15. Citations

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bgc_quast_ppl

Contents

1. Introduction

2. Pipeline summary

3. Quick start

4. Requirements

5. Installation

6. Databases

7. The samplesheet

8. Comparison modes

9. Running the pipeline

Compare samples (default)

Compare tools

Compare to reference

Compare samples with gene cluster families (BiG-SCAPE)

See all parameters in the terminal

10. Parameters

10.1 Input and output

10.2 Comparison with bgc-quast

10.3 BGC prediction: general

10.4 antiSMASH

10.5 DeepBGC

10.6 GECCO

10.7 BiG-SCAPE (gene cluster families)

10.8 Gene annotation

10.9 Resources

10.10 Other options

11. Output

12. Important notes

13. Resuming a run

14. Troubleshooting

15. Citations

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