Funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
When working with haploid assemblies, sometimes you want to remove some repetitive contigs that are contained in other scaffolds of the assembly. If the repeats are indeed unique, then we want to keep them in the assembly. Funannotate can help “clean” up repetitive contigs in your assembly. This is done using a “leave one out” methodology using minimap2 or mummer (nucmer), where the the shortest contigs/scaffolds are aligned to the rest of the assembly to determine if it is repetitive. The script loops through the contigs starting with the shortest and workings its way to the N50 of the assembly, dropping contigs/scaffolds that are greater than the percent coverage of overlap (--cov) and the percent identity of overlap (--pident).