Hello,

We have developed a gene annotator called FINDER which can annotate eukaryotic genomes using short-read RNA-Seq reads and protein sequences. It is completely automated and requires no manual intervention. FINDER also runs BRAKER to incorporate predicted genes in the repertoire. You can access the paper from FINDER and the software from here GitHub.

Thank you.

The easiest way is to use MOSGA, a freely modern and easy-to-use eukaryotic genome annotation tool. It runs online (or you can set it up manually or as a Docker container) with no need for command-line tools: https://mosga.mathematik.uni-marburg.de

Gene predictions can be performed via ab initio, RNA-Seq or proteins, or orthology-based evidence.

Otherwise, you can check:

• Yandell, M., & Ence, D. (2012). A beginner’s guide to eukaryotic genome annotation. Nature Reviews Genetics, 13(5), 329–342. https://doi.org/10.1038/nrg3174
• Jung, H., Ventura, T., Chung, J. S., Kim, W.-J., Nam, B.-H., Kong, H. J., Kim, Y.-O., Jeon, M.-S., & Eyun, S. (2020). Twelve quick steps for genome assembly and annotation in the classroom. PLOS Computational Biology, 16(11), e1008325. https://doi.org/10.1371/journal.pcbi.1008325