CAMISIM

CAMISIM is a microbial community and metagenome simulator to address the need for comprehensive and versatile benchmark data sets to evaluate metagenomic analysis software. Recognizing the vast diversity present in shotgun metagenome datasets—stemming from natural biological variability, laboratory protocol differences, replicate numbers, and sequencing technologies—CAMISIM offers a solution for creating standardized yet highly customizable, simulated metagenomic data.

The software can model various microbial abundance profiles, including multi-sample time series and differential abundance studies. It incorporates real and simulated strain-level diversity, providing a realistic approximation of microbial communities. CAMISIM can generate sequencing data reflective of second-and third-generation sequencing technologies based on taxonomic profiles or from scratch (de novo), making it a powerful tool for simulating a broad spectrum of metagenomic data scenarios.

A key feature of CAMISIM is its ability to create gold standards for several critical metagenomic analyses, including sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. These gold standards are essential for the objective assessment of metagenomic analysis tools, offering benchmarks against which the performance of these tools can be measured.

CAMISIM was utilized to generate the benchmark data sets for the first Critical Assessment of Metagenome Interpretation (CAMI) challenge, highlighting its utility and acceptance within the scientific community. Further demonstrating its capabilities, CAMISIM simulated multi-sample data sets of the human and mouse gut microbiomes, achieving high functional congruence with real data. The software has also been applied to explore the impacts of various factors such as evolutionary genome divergence, sequencing depth, and read error profiles on the performance of popular metagenome assemblers like MEGAHIT and metaSPAdes.