This repository contains scripts used for benchmarking Sentieon DNAseq and DNAscope pipelines on AWS EC2.
The script at misc/instance_setup.sh performs initial setup of the instance and download/installation of software packages used in the benchmark.
Input datasets for the benchmark are recorded in the config/config.yaml (and config/config_arm.yaml) files. With the exception of the Element dataset, the pipeline will automatic download input files. Visiting the Element web page recorded in the config file using an internet browser is required for downloading the Element dataset.
The script at misc/run_benchmarks.sh was used to run the benchmarks. Before running the scripts, the SENTIEON_LICENSE variable inside the script should be properly set.