ENEO (pronunced /eˈnɛjo/) is a Snakemake workflow developed for detecting immunogenic neoantigens arising from somatic mutations using only bulk tumor RNA-seq, without requiring matching samples or additional genomic data (WES/WGS). It uses a probabilistic model that leverages population genetics databases and genotype likelihoods to discriminate germline variants from the call set. Additional details are reported in the bioRxiv preprint.
Pipeline documentation is available at https://ctglab.github.io/ENEO
If you used this workflow in your work, don't forget to give credit to the authors by citing the original publication
Tatoni, D., Dalsass, M., Brunelli, G., Grandi, G., Chiariello, M., & D'Aurizio, R. (2024). Efficient and effective identification of cancer neoantigens from tumor only RNA-seq. bioRxiv, 2024-08.