README.md

MeSS figures

This repo contains supplementary code and figures for our paper describing MeSS.

Steps to reproduce the paper's figures are in the following jupyter notebooks:

• 1_download_and_classify.ipynb : Download HMP reads and classify them with Kraken2 and Bracken.
• 2_simulate_reads.ipynb : Simulate CAMISIM and MeSS reads from the previously obtained Bracken abundances.
• 3_plot_diversities.ipynb: Plot alpha and beta diversities for simulated and real abundances.
• 4_plot_resource_usage.ipynb: Plot RAM and CPU usage for CAMISIM and MeSS.

Dependencies

Install conda

You need a conda (Miniforge) install to run the notebooks:

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Create conda env

mamba env create -n notebooks -f env.yaml

Run jupyter lab

mamba activate notebooks
jupyter lab

Figures

Diversities

Figure 1A

Figure 1B

Figure S1

Benchmark

Figure S2

Figure S3