Bakta annotations for 1 991 NORM hybrid assemblies

Contains bakta annotations for 1 991 Escherichia coli hybrid assemblies used in a study into co-evolution between colibactin production and resistance. Files The archive `bakta-annotations-ecoli.tar` extracts to a folder `bakta-annotations-ecoli` with 1 991 folders each containing the gzipped output files from bakta for each assembly. Extracted size is the same as the upload size. Accession numbers and other metadata for the assemblies are available in the `NORM-hybrid_metadata.tsv` file. Data related to colibactin production and resistance are available in a separate upload: doi: 10.5281/zenodo.17017465. Methods Data were obtained from two studies [1] and [2] and annotated with bakta v1.10.4 (GitHub: oschwengers/bakta, [3]) against full database v5.1 dated 2024-01-19 (doi: 10.5281/zenodo.10522951). Bakta was ran using the following command:```bakta --db $bakta_db --tmp-dir $tmpdir --min-contig-length 200 --prefix $basename --output $outdir --threads $threads $fasta``` Data source Hybrid assembly files are available from the European Nucleotide Archive under project accessions PRJEB57633 and PRJEB45354. The list of assemblies included in this upload is included in the `NORM-hybrid_metadata.tsv` file. References Isolation, sequencing, and assembly are described in the following two studies: [1] Gladstone et al. "Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study". The Lancet Microbe (2021). doi: 10.1016/S2666-5247(21)00031-8. [2] Arredondo-Alonso et al. "Plasmid-driven strategies for clone success in Escherichia coli". Nature Communications (2025). doi: 10.1038/s41467-025-57940-1. If you use these assemblies, you should also cite the publication describing Bakta: [3] Schwengers et al. "Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification." Microbial genomics (2021). doi: 10.1099/mgen.0.000685.