The German Network for Bioinformatics Infrastructure – de.NBI is a national, academic, and non-profit research infrastructure initiated in 2015 by the Federal Ministry of Education and Research. Within de.NBI, the Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi) supports scientists with bioinformatics software tools, pipelines and resources for microbial research with a focus on the analysis of microbial genomes, metagenomes, and related datasets.
In the last decade, various software tools, pipelines and platforms for annotation, characterization and comparative analysis of genomic as well as metagenomic sequencing data have been maintained and further developed based on feedback from our growing user community. For the comprehensive annotation of microbial genomes, the fully-automated annotation software tool Bakta was developed. Bakta is available as command line tool as well as via a user-friendly web version. Bakta quickly emerged to be one of the most-actively used annotation tools worldwide. For the comparative analysis of bacterial genomes, we maintain the de.NBI flagship tool EDGAR which provides public as well as custom, password protected databases with more than 100,000 included genomes. Furthermore, a broad range of more specialized software tools were developed and maintained, e.g. Platon for the detection of plasmid-borne contigs within draft genomes, ReferenceSeeker for the taxonomic classification of microbial genomes, and MGX2 for the processing and analysis of metagenomic data. A further important project is the large-scale bacterial genome repository BakRep, which provides access to a comprehensive assembly and annotation data, enriched with taxonomic information, for a total of ~2.4 million genomes.
Besides the development and maintenance of analysis software and data resources, BiGi also hosts a branch of the federated de.NBI cloud, which provides large-scale compute resources to the scientific community on demand. Additionally, BiGi offers training programs, workshops and user support to help the scientific community to use the various bioinformatics solutions effectively in their research.
In summary, the microbial researcher community can strongly benefit from the triplet of services provided by BiGi:
A broad set of well-maintained and constantly improved software solutionsAn accessible powerful and growing cloud-computing infrastructureA regular offer of accompanying workshops and training courses