Benchmarking and evaluation of the HoCoRT Python package. Illumina HiSeq and MiSeq, and Nanopore simulated datasets (1% and 50% host contamination) are generated using InSilicoSeq and NanoSim. The different HoCoRT pipelines are then tested and benchmarked.
First create the conda environment and activate it:
conda env create -f environment.yaml
conda activate hocort-eval
Run the evaluation tests by running the following command:
snakemake --cores 16
The results will be available in the directories named hiseq_reads, miseq_reads and nanopore_reads.
The boxplot generation script is found under "/boxplots/".