PROBEAT

PROBEAT (PRObiotic Bacterial gEnome Analysis Toolkit) is a Dockerized Snakemake workflow for bacterial isolate genome analysis with a probiotic interpretation layer, Streamlit web UI, Redis worker, and HTML/PDF reporting.

This repository documents the full Docker profile only. The full profile builds the complete runtime image for Illumina PE/SE, Oxford Nanopore ONT, and HYBRID analyses.

✨📘 VIEW SAMPLE PDF BOOKLET REPORT✨

Workflow Programs

PROBEAT combines FastQC, fastp, Rasusa, Unicycler, Flye, Medaka, QUAST, Mash, sourmash, BUSCO, Bakta, AMRFinderPlus, ABRicate, KofamScan, KEGGDecoder, dbCAN, eggNOG-mapper, antiSMASH, gutSMASH, BAGEL4, geNomad, GenomeSPOT, FastANI, MOB-suite, GOProbioticProfiler, pyCirclize, and custom reporting scripts to cover QC, assembly, taxonomy, annotation, safety, mobile elements, functional potential, probiotic markers, comparative genomics, genome maps, and final HTML/PDF reports.

Requirements

• Docker Engine with Docker Compose (docker-compose)
• Internet access for the first image build and database download
• Sufficient disk space for the full image, workflow outputs, and downloaded biological databases (the workflow and databases require about 200 GB of disk space)
• Linux server or workstation recommended for production runs

The databases are not stored in Git and are not baked into the image. They are downloaded into ./storage/databases by the database-init Compose service.

Largest database groups:

• bakta_full: 84G
• eggnog: 59G
• antismash: 9.4G
• dbcan_v5: 7.4G
• kofam: 7.2G
• gutsmash: 3.8G

Medium-sized database groups:

• mob_suite: 2.9G
• sourmash: 2.9G
• dbcan: 2.3G
• fastani_ncbi: 1.8G
• genomad: 1.4G

Quickstart

Clone the repository:

git clone https://github.com/vebaev/PROBEAT.git
cd PROBEAT

Create the local environment file:

cp .env.example .env

Build the full Docker image:

docker build --build-arg INSTALL_PROFILE=full -t probeat:full .

Download all required databases:

docker-compose run --rm database-init

Verify the downloaded databases:

docker-compose run --rm database-manager

Start the application stack:

docker-compose up -d redis worker streamlit

Check that the web UI is healthy:

curl http://localhost:9797/_stcore/health

Open the interface:

http://localhost:9797

Validate Installation

Run the full runtime doctor:

docker-compose run --rm worker ./probeat doctor --profile full --strict

Run a Snakemake dry-run with the bundled smoke FASTQ:

docker-compose run --rm worker \
  workflow/run_sample.sh SMOKE_SE SE tests/data/smoke.fastq \
  --dry-run --cores 2

Data Locations

The default .env.example keeps runtime data under ./storage:

• ./storage/uploads: uploaded FASTQ files
• ./storage/results: workflow outputs and reports
• ./storage/databases: downloaded biological databases
• ./storage/logs: workflow and service logs
• ./storage/state: job state files

These directories are intentionally ignored by Git.

Troubleshooting

Check container status:

docker-compose ps

Check Streamlit logs:

docker logs --tail=120 probeat-streamlit-1

Check worker logs:

docker logs --tail=120 probeat-worker-1

Re-run database verification:

docker-compose run --rm database-manager

If a workflow step fails, inspect:

storage/results/<sample>/run/probeat.log
storage/logs/

License

See LICENSE.

Citation

See CITATION.cff.

Workflow Tool Sources

Workflow Tool	Purpose	Output	Source Repository
fastp 1.3.3	Read trimming	FASTQ QC	https://github.com/OpenGene/fastp
Porechop 0.2.4	Adapter removal	Trimmed FASTQ	https://github.com/rrwick/Porechop
Rasusa 2.1.0	Coverage normalization	Subsampled FASTQ	https://github.com/mbhall88/rasusa
Unicycler 0.5.1	Short/hybrid assembly	Assembly FASTA	https://github.com/rrwick/Unicycler
Flye 2.9.6	ONT assembly	Assembly FASTA	https://github.com/mikolmogorov/Flye
Medaka 2.x	Consensus polishing	Polished FASTA	https://github.com/nanoporetech/medaka
QUAST 5.3.0	Assembly statistics	Quality table	https://github.com/ablab/quast
BUSCO 6.0.0	Completeness assessment	BUSCO summary	https://gitlab.com/ezlab/busco
Mash 2.3; sourmash 4.9	Reference matching	Top-hit tables	https://github.com/marbl/Mash; https://github.com/sourmash-bio/sourmash
FastANI 1.34	ANI comparison	ANI table/heatmap	https://github.com/ParBLiSS/FastANI
Bakta 1.12.0	Feature annotation	GFF3/FAA/TSV	https://github.com/oschwengers/bakta
eggNOG-mapper 2.1.x	Function assignment	Annotation table	https://github.com/eggnogdb/eggnog-mapper
KOfamScan 1.3.0	KO assignment	KO table	https://github.com/takaram/kofam_scan
KEGGDecoder 1.3	Pathway completeness	Table/SVG	https://github.com/bjtully/BioData/tree/master/KEGGDecoder
dbCAN 5.2.9	Carbohydrate profiling	CAZyme/CGC tables	https://github.com/bcb-unl/run_dbcan
AMRFinderPlus 4.2.7	Resistance detection	AMR table	https://github.com/ncbi/amr
ABRicate 1.0.1	Gene screening	Hit tables	https://github.com/tseemann/abricate
MOB-suite 3.1.9	Plasmid classification	Contig report	https://github.com/phac-nml/mob-suite
geNomad 1.x	MGE detection	Plasmid/virus tables	https://github.com/apcamargo/genomad
BAGEL4	Bacteriocin detection	Cluster table	https://github.com/vanheel/BAGEL4
antiSMASH 8.0.4	BGC detection	Region table	https://github.com/antismash/antismash
gutSMASH	Cluster detection	Region table	https://github.com/victoriapascal/gutsmash
GenomeSPOT	Condition prediction	Prediction table	https://github.com/cultivarium/GenomeSPOT
PGMDB	Marker detection	Marker summary hits	https://github.com/vebaev/PROBEAT
GOProbiotic 1.0.0	Functional profiling	GO tables/plots	https://github.com/vebaev/PROBEAT
pyCirclize	Circular mapping	PNG/SVG map	https://github.com/moshi4/pyCirclize
MultiQC 1.35	Report aggregation	HTML report	https://github.com/MultiQC/MultiQC