BakRep

BakRep is a searchable large-scale web repository for bacterial genomes enriched with standardized genome characterizations and related metadata. Researchers can query this repository via a flexible search engine thus combining genomic information and metadata.

Description

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. We truly believe that this large-scale but accessible genome web repository will help microbiology researchers from various fields to exploit this vast amount of genomes by compiling subsets as a starting point for their targeted analyses. Its user-friendly interface and extensive dataset make it an invaluable resource for the scientific community, supporting a wide range of comparative and clinical studies and driving new discoveries in microbial genomics.

Search Engine

To ensure the accessibility of out results, all data was stored in a public S3 bucket. Furthermore, an interactive web page is provided to make the data available. To furnish users with an extensive yet adaptable search, our repository provides an advanced search function that enables robust but flexible and scalable queries by values like genome size, GC content, number of contigs, sequence type, different taxonomic ranks as well as the metadata associated with each dataset.

Web: bakrep.computational.bio
CLI:  github.com/ag-computational-bio/bakrep-cli