Comprehensive simulation of metagenomic sequencing data with non-uniform sampling distribution

Abstract

Background: Metagenomic sequencing is a complex sampling procedure from unknown mixtures of many genomes. Having metagenome data with known genome compositions is essential for both benchmarking bioinformatics software and for investigating influences of various factors on the data. Compared to data from real microbiome samples or from defined microbial mock community, simulated data with proper computational models are better for the purpose as they provide more flexibility for controlling multiple factors.

Methods: We developed a non-uniform metagenomic sequencing simulation system (nuMetaSim) that is capable of mimicking various factors in real metagenomic sequencing to reflect multiple properties of real data with customizable parameter settings.

Results: We generated 9 comprehensive metagenomic datasets with different composition complexity from of 203 bacterial genomes and 2 archaeal genomes related with human intestine system.

Conclusion: The data can serve as benchmarks for comparing performance of different methods at different situations, and the software package allows users to generate simulation data that can better reflect the specific properties in their scenarios.

Graphical abstract

Keywords

simulation / metagenomic sequencing data / non-uniform sampling / nuMetaSim

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ACKNOWLEDGEMENTS

We thank Dr. Hongfei Cui for her comments on the simulation design. This work is partially supported by the National Natural Science Foundation of China (Nos. 61673231 and 61721003).

COMPLIANCE WITH ETHICS GUIDELINES

The authors Shansong Liu, Kui Hua, Sijie Chen and Xuegong Zhang declare that they have no conflict of interests.ƒThis article does not contain any studies with human or animal subjects performed by any of the authors.

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