benchmark-MeSS-CAMISIM

This repo contains the nextflow pipeline to benchmark CAMISIM and MeSS, two metagenomic communities simulators.

The pipeline is used to generate figures data from our paper describing MeSS.

Setup NCBI API key

Go to https://www.ncbi.nlm.nih.gov/account/login/ to create an NCBI account and get an API key.

Before launching the pipeline set your key as a secret:

nextflow secrets set NCBI_KEY 0123456789abcdef

Run the pipeline

Using the example tables in data

nextflow run main.nf --input data -params-file run-params.yml

Subsets piepeline

You can download a total set of genomes from a given taxon (bacteria for example), and run CAMISIM and MeSS on subsamples of that set.

For example, download 6 bacterial reference genomes and simulate reads at 1X coverage depth for 1,2,3 subsets:

nextflow run main.nf -params-file subsets-params.yml --total 6 --subsets 1,2,3 --outdir subsets