STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Metagenomic analysis resolution is increasing, driving focus on microbial genome evolution in longitudinal data.
• Existing software simulates microbial communities at the strain level, but lacks within-strain evolutionary signal simulation for longitudinal samples.

Purpose of the Study:

• To introduce STEMSIM, a user-friendly command-line simulator for short-term evolutionary mutations in longitudinal metagenomic data.
• To provide a tool for evaluating analytical methods designed to detect within-strain evolutionary signals.

Main Methods:

• STEMSIM accepts simulated longitudinal raw sequencing reads (microbial communities or single species) as input.
• The simulator outputs modified reads incorporating within-strain evolutionary mutations and associated mutation data.

Main Results:

• STEMSIM effectively simulates within-strain evolutionary mutations in longitudinal metagenomic data.
• The tool generates modified sequencing reads and detailed mutation information.

Conclusions:

• STEMSIM addresses the lack of tools for simulating within-strain evolutionary signals in longitudinal metagenomic datasets.
• This simulator is valuable for assessing the performance of bioinformatics tools in analyzing microbial evolution.