Whole genome sequencing for the characterization of bacterial genomes presents several bioinformatics challenges. Primary outcomes include determining sequencing read quality, performing alignment and de novo assembly of the bacterial genome, annotating the processed genomes, and discovering genomic features of interest. Due to the specificity of genetic elements within each bacterial genus, separate workflows must be utilized for each bacterial species of interest. This Nextflow pipeline aims to characterize bacteria of interest to food safety in poultry broiler production systems, specifically Salmonella enterica Heidelberg, Enterococcus faecalis, and their respective plasmids. Alignment, de novo assembly, and marker-based detection of genetic elements of interest are included in the pipeline, and a variety of custom databases have been created to aid in the annotation of the resulting genomic sequences. For more information, explore the pipeline through the links below.