The following is a shortened version of the reproducible workflow for generating the R. pomeroyi databases. A longer workflow with additional detail is included in the datapack when downloading the databases from Zenodo. (Zenodo link: https://zenodo.org/record/7439166#.Y7tgZ-zMJQ0)
The databases were created using anvio v7.1-dev. First, the contigs database was generated from the genome sequence fasta file and a file describing each gene call. Curated functional annotations from the Moran Lab (including the TnSeq mutants) were imported from tab-delimited files describing each annotation, and automatic functional annotations were added by running various annotation programs.
# make the database
anvi-gen-contigs-database -f R-pom_genome.fasta --external-gene-calls DSS3_external_gene_calls_NEW.txt --skip-predict-frame -n R_POMEROYI_DSS3 -o R_POM_DSS