BakRep
BakRep is a comprehensive, scalable web repository that aggregates and standardizes millions of publicly available bacterial genomes from e.g. AllTheBacteria. Each genome is enriched with uniform quality metrics, taxonomic classification, sequence typing, and annotation, enabling rapid and reproducible comparative analyses across large datasets, and integrated with accompanying submission metadata.
Key Benefits
- Extensive data coverage with consistently processed bacterial genomes.
- Integrated Metadata: original submission metadata comprising e.g. sampling location, data, source.
- Standardized genome characterizations, including QC, taxonomy, MLST, and annotation.
- Powerful search and filtering to compile custom genome sets based on genomic or metadata attributes.
- Web interface and command-line access for both exploratory and automated high-throughput workflows.
Features
- Unified pipeline for QC, taxonomic assignment, sequence typing, and annotation.
- Advanced search by species, genome size, GC content, contig count, sequence type, and more.
- Downloadable genome subsets for downstream computational analyses.
- CLI integration for large-scale or reproducible workflows.
Applications
- Comparative genomics, phylogenetics, and population genomics.
- Large-scale surveys of resistance genes, virulence factors, or metabolic traits.
- Building curated genome datasets for benchmarking or tool development.
- Supporting epidemiological investigations and outbreak analyses.
Intended Use
BakRep is ideal for microbial genomics researchers, bioinformaticians, and epidemiologists who need reliable, standardized access to large bacterial genome collections.
No de.NBI funding