Dnaapler: a tool to reorient circular microbial genomes

Microorganisms found in natural environments are fundamental components of ecosystems and play vital roles in various ecological processes. Studying their genomes can provide valuable insights into the diversity, functionality, and evolution of microbial life, as well as their impacts on human health. Once the genetic material is extracted from environmental samples, it undergoes sequencing using technologies like whole genome sequencing (WGS). The raw sequence data is then analysed, and computational methods are applied to assemble the fragmented sequences and reconstruct the complete microbial genomes.

Many biological entities including Bacteria, Archaea, plasmids, bacteriophages and other viruses can have circular genomes. Once assembled, a circular genome sequence is represented as a linear character string and labelled in some way to indicate that it should be circular. The point at which the linear sequence begins is random, due to the nature of the algorithms employed in assembling genomes from sequencing reads. Such arbitrary startpoints can affect downstream genome annotation and analysis; they may occur within coding sequences (CDS), can disrupt the prediction potential of mobile genetic elements like prophages, and make pangenome analyses based on gene order difficult. Therefore, microbial sequences are often required to be reoriented to begin by convention with certain genes: the dnaA chromosomal replication initiator gene for bacterial chromosomes, the repA plasmid replication initiation gene for plasmids and the terL large terminase subunit gene for bacteriophages. Here we present Dnaapler, a flexible microbial sequence reorientation tool that allows for rapid and consistent orientation of circular microbial genomes such as Bacteria, plasmids and bacteriophages. Dnaapler is hosted on GitHub at github.com/gbouras13/dnaapler.