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Motivation

What ?

MeSS is a snakemake-powered cli for downloading genomes and simulating metagenomes.

Why ?

Shotgun metagenomic samples of microbiota can be a challenge to analyse. In fact, given their intrinsic complexities coupled with technical challenges in the wet-lab, it is difficult to know exactly what is truly present in the sample. Simulating such samples offers a controlled environment allowing to benchmark bioinformatics tools, optimize study design, calcuate statistical power, etc ...

When ?

  • Testing sequencing's detection limit

Let's say, for example, you have a stahpylococcus aureus that is present at roughly 0.01% abundance, and you want to know at which sequencing depth you can detect it. With MeSS you can easily make samples with mixes of genomes at different abundances and sequencing depths for a selected sequencing technology.

  • Benchmarking taxonomic classifiers

MeSS includes read simulators that generate gold standard bam files. This means that you know the origin of every simulated read, and thus know the true composition of the sample. This allows comparing the results of tools like centrifuge or kraken2 against a ground truth dataset.

  • Testing the impact of sequencing technology on genome assembly

Let's suppose that you have a bacterial isolate that you plan to sequence. However, you are not sure about which sequencing technology to use, at which depth, etc ... You can use MeSS to easily to generate reads at different depth, with different sequencing technologies and error profiles (ONT 10.4.1, PacBio hifi, illumina miseq...). Simulated reads can be assembled, and you an evaluate the impact of sequencing variables on your assembly.

Alternatives

CAMISIM is the state-of-the-art shotgun metagenomics simulator. At the time, CAMISIM was slow and it's dependencies had to be installed by hand, so we decided to write our own tool !

Warning

CAMISIM will have an upcoming faster version written in nextflow ! Go check it out at CAMISIM