Hybran: Hybrid Reference Transfer and ab initio Prokaryotic Genome Annotation

De novo assembly has become commonplace for microbial organisms, increasing the demand for reliable genome annotation. Ab initio annotation is not an ideal approach for closely related strains due to suboptimal matching of the short or hypervariable genomic features that reference-based annotation transfer can overcome through identification of conserved synteny. At the same time, reference-based annotation methods leave gaps in the annotation where structural variations introduce unique sequence. We present Hybran, a hybrid reference-based and ab initio prokaryotic genome annotation pipeline that transfers features from a curated reference annotation and supplements unannotated regions with ab initio predictions. It builds on existing tools to create initial annotations using both approaches, then compares and resolves them to produce the hybrid annotation. With this pipeline, full advantage is taken of the communitys experimental efforts on reference strains to propagate as many known features as possible without sacrificing best-effort ab initio predictions for the remaining unannotated loci. Genome annotation performed in this way can facilitate comparative genomics and the investigation of evolutionary dynamics in microbial populations. Hybran is freely available at https://lpcdrp.gitlab.io/hybran