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RAmpSim: A Thermodynamic Simulator for Hybridization Capture in Metagenomic Sequencing.

Aidan Zhang¹, Christina Boucher², Noelle Noyes³

¹Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213.

Biorxiv : the Preprint Server for Biology

|December 22, 2025

Summary

RAmpSim accurately simulates biases in capture-based metagenomics, improving data analysis. This tool models bait hybridization and fragment capture for better benchmarking and bait-set evaluation.

Keywords:

amplification read simulation shotgun metagenomics sequencing thermodynamic modeling

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Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells

Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells

Published on: June 1, 2018

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Hybridization capture with long-read sequencing is vital for metagenomic analysis.
Existing simulators fail to account for systematic biases introduced by bait multiplicity, sequence composition, and species abundance.

Purpose of the Study:

To introduce RAmpSim, a novel simulator for capture-based metagenomic sequencing.
To model biases in bait-target hybridization and fragment capture accurately.

Main Methods:

Utilized a thermodynamic nearest-neighbor energy model and Boltzmann-weighted sampling for bait-target binding.
Employed multinomial sampling for fragment generation, incorporating bait concentration, binding energy, and genomic abundance.
Integrated with existing long-read simulators to model platform-specific errors.

Main Results:

RAmpSim accurately reproduces empirical within-genome coverage and cross-species enrichment patterns.
Simulated coverage distributions showed an order of magnitude improvement over uniform baselines using earth mover's distance.
Classification analysis demonstrated high recall in high-coverage regions, outperforming uniform baselines.

Conclusions:

RAmpSim provides an efficient and interpretable framework for simulating capture-based metagenomic sequencing.
The simulator supports accurate benchmarking and evaluation of bait sets.
RAmpSim enhances the reliability of metagenomic data analysis by accounting for critical biases.