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/".