SUMMARY

This folder is a package that contains scripts and files required for running one experiment: BLAST, MASH, and VAPOR simulated read classification.

REQUIREMENTS

    Python3.x
    BLAST (makeblastdb, blastn) 2.7.1+
    MASH 2.0
    VAPOR v1.0+
    GNU parallel 20160222

Additionally, artificialFastqGenerator (afg) v1.0.0 must be placed in code/afg

Additionally, the following resources are required:

refs/: a set of used resources with accompanying MASH sketch and BLAST databases:
    HA_A_allsp_nfu_nospaces.fa

These can be downloaded from https://s3.climb.ac.uk/vapor-benchmark-data/benchmarking_simulation_refs_06_03_19.tar.gz

For plotting, pandas 0.23.4, matplotlib 2.2.3, NumPy 1.15.2, and seaborn 0.9.0 are required.

USAGE

Run the benchmarks with N processes:

    parallel --jobs N < code/parallel_commands/simulate_and_classify_commands.pcom.sh > logs/simulate_and_classify_commands.log 2>&1

Collect and plot the results with:

    bash code/retrieve_results.sh > results.csv
    python3 plotting/plot_simulation_boxes.py results.csv