Automated Bacterial Genome Annotation & BGC Discovery Pipeline
CoGe-Pipeline is an end-to-end, automated bioinformatics pipeline developed for large-scale bacterial genome analysis and secondary metabolite discovery. It was designed as part of the One Day One Genome (ODOG) initiative to process 25–30 bacterial genomes in a reproducible, scalable, and fault-tolerant manner.
The pipeline takes paired-end Illumina reads as input and produces:
- High-quality genome assemblies
- Functional annotations
- Biosynthetic gene cluster (BGC) predictions
- Comparative BGC clustering results
Paired-end FASTQ
├── FastQC (raw QC)
├── fastp (trimming & filtering)
├── FastQC (post-trim QC)
├── SPAdes (genome assembly)
├── QUAST (assembly quality)
├── Prokka (genome annotation)
├── antiSMASH (BGC prediction)
└── BiG-SCAPE (comparative BGC clustering)
- Fully automated end-to-end workflow
- Handles multiple genomes in a single run
- Robust error handling (failed genomes are skipped, pipeline continues)
- Resume-friendly: completed steps are not recomputed
- Conda-based reproducible environments
- Supports comparative BGC analysis across all genomes
- Generates interactive BiG-SCAPE HTML visualizations
| Tool | Purpose | Citation |
|---|---|---|
| FastQC | Read quality control | Andrews S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data |
| fastp | Read trimming & filtering | Chen et al. (2018). Bioinformatics, 34(17):i884-i890. DOI:10.1093/bioinformatics/bty560 |
| SPAdes | De novo genome assembly | Bankevich et al. (2012). J Comput Biol, 19(5):455-477. DOI:10.1089/cmb.2012.0021 |
| QUAST | Assembly quality assessment | Gurevich et al. (2013). Bioinformatics, 29(8):1072-1075. DOI:10.1093/bioinformatics/btt086 |
| Prokka | Genome annotation | Seemann T. (2014). Bioinformatics, 30(14):2068-2069. DOI:10.1093/bioinformatics/btu153 |
| antiSMASH | Biosynthetic gene cluster detection | Blin et al. (2023). Nucleic Acids Res, 51(W1):W46-W50. DOI:10.1093/nar/gkad344 |
| BiG-SCAPE | BGC clustering & network analysis | Navarro-Muñoz et al. (2020). Nat Chem Biol, 16:60-68. DOI:10.1038/s41589-019-0400-9 |
Paired-end Illumina FASTQ files:
sample_R1.fastq.gz
sample_R2.fastq.gz
Important: Sample names must NOT contain spaces or special characters.
results/
├── sample1/
│ ├── fastqc_raw/
│ ├── fastp_output/
│ ├── spades_output/
│ ├── quast_output/
│ ├── prokka_output/
│ └── antismash_output/
├── bigscape_output/
│ ├── index.html
│ ├── network files
│ └── GCF results
└── logs/
A dedicated installation script is provided to:
- Detect or install Conda automatically
- Create required Conda environments
- Install all dependencies (antiSMASH DBs, Pfam, BiG-SCAPE requirements)
bash install.shRun the pipeline from the directory containing FASTQ files:
bash genome_pipeline.shBiG-SCAPE is executed once after all genomes are processed, enabling comparative analysis across the full dataset.
- antiSMASH outputs identify BGCs per genome
- BiG-SCAPE outputs cluster BGCs into Gene Cluster Families (GCFs)
- Interactive visualization available via:
results/bigscape_output/index.html
- Comparative bacterial genomics
- Natural product & secondary metabolite discovery
- Antibiotic and bioactive compound mining
- Functional genomics research
- Large-scale genome annotation projects
- AI-based BGC novelty prediction
- Bioactivity prediction models
- Automated genome & BGC summary reports
- Integration with metabolomics (LC-MS/MS)
If you use CoGe-Pipeline in your research, please cite:
CoGe-Pipeline: Automated Bacterial Genome Annotation & BGC Discovery Pipeline
One Day One Genome (ODOG) Initiative
Bharat Genome Database (BGDB)
Navaneeth S Raju
2025. Available at: https://github.com/neonnav/CoGe
Additionally, please cite all the tools used in the pipeline (see Tools table above).
Developed by Navaneeth S Raju as part of the One Day One Genome (ODOG) project
This project is released under the MIT License.
For issues, questions, or contributions, please open an issue on GitHub or contact the BGDB team.
If you find this pipeline useful, please consider starring the repository!