There are many 'best practises' papers by now, the exact paper depends on your species (bacterium? plant?) and your technology (2nd generation? 3rd generation? Hybrid? 10x?)

Ten steps to get started in Genome Assembly and Annotation https://f1000research.com/articles/7-148/v1

A beginner’s guide to eukaryotic genome annotation http://www.yandell-lab.org/publications/pdf/euk_genome_annotation_review.pdf

The BRAKER paper Supplementary Materials are also useful; https://academic.oup.com/bioinformatics/article/32/5/767/1744611

And if your interest lies in repetitive elements of the genome, look at The case for not masking away repetitive DNA from Keith Slotkin: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-018-0120-9

here is another good starting point : Ten steps to get started in Genome Assembly and Annotation