Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany.
Microb Genom. 2024 Oct;10(10). doi: 10.1099/mgen.0.001305.
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.
由于无数原因，细菌是许多学科中令人着迷的研究对象，而全基因组测序（WGS）已成为推进微生物学理解的首要方法。同时，能够获得具有成本效益的测序平台加速了细菌 WGS 的发展，达到了前所未有的水平，这在数据可及性、计算需求、分析工作流程的异质性以及最终其科学可用性方面带来了新的挑战。为此，先前的一项研究发布了截至 2018 年 11 月从欧洲核苷酸档案库中获得的 661405 个细菌基因组组装的统一处理数据集。在此基础上，我们进行了进一步的基于基因组的分析，如分类学分类、多位点序列分型和所有基因组的注释。在这里，我们展示了 BakRep，这是一个可搜索的大规模网络存储库，其中包含这些基因组的丰富信息，包括一致的基因组特征和原始元数据。该平台提供了一个灵活的搜索引擎，结合了分类学、基因组和元数据信息，以及用于可视化基因组特征的交互元素。此外，所有结果都可以通过附带的命令行工具下载进行离线分析。该网络存储库可通过 https://bakrep.computational.bio 访问。
