STEMSIM

STEMSIM simulates short-term evolutionary mutations within microbial strains in longitudinal metagenomic datasets to generate modified sequencing reads and mutation annotations for benchmarking and analysis.

Key Features:

• Simulation of evolutionary mutations: Simulates short-term within-strain evolutionary mutations in longitudinal metagenomic data.
• Input specifications: Accepts simulated longitudinal raw sequencing reads from complex microbial communities or single species.
• Output specifications: Generates modified reads that incorporate within-strain evolutionary mutations and produces detailed information about those mutations.
• Benchmarking output: Produces simulated evolutionary changes suitable for evaluating and benchmarking analytic tools that detect short-term evolutionary mutations in metagenomic datasets.

Scientific Applications:

• Method evaluation: Evaluation and benchmarking of computational methods for detecting short-term evolutionary mutations in longitudinal metagenomic datasets.
• Microbial evolution studies: Investigation of microbial evolution and adaptive mechanisms in complex microbial communities over time.

Methodology:

Accepts simulated longitudinal raw sequencing reads and modifies them to incorporate within-strain evolutionary mutations, outputting modified reads together with detailed mutation information.