MetaSim

MetaSim simulates synthetic sequencing reads from specified genomes to reproduce taxonomic diversity in metagenomic datasets for benchmarking and experimental design using NCBI taxonomy and next-generation sequencing technologies.

Key Features:

• Synthetic Read Generation: Generates synthetic read collections that reflect the complex taxonomical composition of metagenomic datasets.
• Customizable Metagenome Design: Allows specification of the number of genomes present at various levels within the NCBI taxonomy to create tailored metagenomes.
• Sequencing Technology Simulation: Simulates sequencing reads with characteristics of multiple sequencing technologies, including next-generation sequencing platforms.
• Population Sampling with Evolutionary Context: Includes an optional population sampler that produces evolved sequences from source genomes according to a user-defined evolutionary tree.
• Genome Reference Database: Operates from a database of specified genomes used as the foundation for read sampling and abundance assignments.

Scientific Applications:

• Benchmarking and Tool Development: Provides standardized simulated read datasets for benchmarking metagenomic software and evaluating analysis approaches.
• Experimental Design and Project Planning: Assists planning of metagenomic sequencing projects by simulating expected taxonomic compositions and sequencing outputs.
• Testing Evolutionary and Population Scenarios: Enables evaluation of evolutionary dynamics by generating evolved sequences along a defined evolutionary tree.

Methodology:

MetaSim uses a database of specified genomes; users input parameters defining taxonomical structure and abundance; the software simulates sequencing reads reflecting characteristics of selected sequencing technologies; an optional population sampler evolves sequences according to a provided evolutionary tree.