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Updated: Jul 31, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
1Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA.
Motivation:
As the resolution of metagenomic analysis increases, the evolution of microbial genomes in longitudinal metagenomic data has become a research focus. Some software has been developed for the simulation of complex microbial communities at the strain level. However, the tool for simulating within-strain evolutionary signals in longitudinal samples is still lacking.
Results:
In this study, we introduce STEMSIM, a user-friendly command-line simulator of short-term evolutionary mutations for longitudinal metagenomic data. The input is simulated longitudinal raw sequencing reads of microbial communities or single species. The output is the modified reads with within-strain evolutionary mutations and the relevant information of these mutations. STEMSIM will be of great use for the evaluation of analytic tools that detect short-term evolutionary mutations in metagenomic data.
Availability And Implementation:
STEMSIM and its tutorial are freely available online at https://github.com/BoyanZhou/STEMSim.
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