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Microbial Genomics logo Microbial Genomics

Volume 10, Issue 10

BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata Open Access

Abstract

Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding. Meanwhile, access to cost-effective sequencing platforms has accelerated bacterial WGS to unprecedented levels, introducing new challenges in terms of data accessibility, computational demands, heterogeneity of analysis workflows and, thus, ultimately its scientific usability. To this end, a previous study released a uniformly processed set of 661 405 bacterial genome assemblies obtained from the European Nucleotide Archive as of November 2018. Building on these accomplishments, we conducted further genome-based analyses like taxonomic classification, multilocus sequence typing and annotation of all genomes. 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. The web repository is accessible via https://bakrep.computational.bio.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): annotation , bacteria , big data , computational biology , multilocus sequence typing , taxonomic classification and whole-genome sequencing
Funding
This study was supported by the:
  • German Network for Bioinformatics Infrastructure (Award 031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A)
    • Principal Award Recipient: AlexanderGoesmann
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-10-30
2025-12-07

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/content/journal/mgen/10.1099/mgen.0.001305
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BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata
M Gen 10, 001305 (2024); https://doi.org/10.1099/mgen.0.001305
/content/journal/mgen/10.1099/mgen.0.001305
/content/journal/mgen/10.1099/mgen.0.001305
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