Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes.

ABSTRACT: Here, we introduce a new annotation pipeline, called Eukan, designed to deliver reliably high-quality results across a broad range of eukaryotes. First, experimental evidence is automatically leveraged to refine predictions, specifically, RNA-Seq coverage to inform generalized Hidden Markov Model gene prediction and intron lengths to inform protein sequence alignments. Second, a consensus is created from an empirically optimized weighting of gene predictions from multiple sources. Third, Eukan runs a post-annotation routine to recover gene predictions missing from the consensus that otherwise have strong transcript support and appear to be protein-coding. We compare the results of Eukan with those of three popular freely available pipelines (Maker, Braker, and Gemoma) on 17 phylogeneticall

SUBMITTER: Sarrasin M 

PROVIDER: S-EPMC12817076 | biostudies-literature | 2026 Mar

REPOSITORIES: biostudies-literature