BakRep – A searchable large-scale web repository for bacterial genomes, characterizations and metadata
More than 640,000 bacterial genomes, uniformly processed & characterized, enriched with metadata, accessible via a flexible search engine - genomic information at your fingertips!
Background
Public databases are brimming with bacterial WGS data posing a genetic treasure for many different applications.
However, most analyses focus on particular tiny subgroups that are hard to establish from raw sequencing data or metadata, only.
To this end, BakRep (Denglish blend of Bakterien & Repository) provides access to both comprehensive standardized genome characterizations and metadata via a flexible search engine.
BakRep comprises assembly QC metrics, robust taxonomic classifications, MLST typing, genome annotations and original metadata for a precious collection of bacterial genomes assembled by Blackwell et al.
Results
Here we present BakRep, a searchable large-scale web repository of these genomes enriched with consistent genome characterizations and original metadata.
The platform provides a flexible search engine combining taxonomic, genomic and metadata information, as well as interactive elements to visualize genomic features.
Furthermore, all results can be downloaded for offline analyses via an accompanying command line tool.
Our long-term plan includes the addition of more genomes to our repository, aiming for the continuous expansion of this standardized dataset.
We envision BakRep as a high-quality open resource for microbial researchers worldwide.
Availability
Citation
Fenske L., Jelonek L., Goesmann A., Schwengers O. (2024)
BakRep – A searchable large-scale web repository for bacterial genomes, characterizations and metadata.
bioRxiv doi: doi.org/10.1101/2024.05.28.596065