ReSeqSim

ReSeqSim simulates and evaluates combinations of sequencing technologies to optimize comparative genome re-sequencing, with a focus on reconstructing large structural variants (SVs) in the human genome.

Key Features:

• Technology Integration: Simulates optimal combinations of medium and short read sequencing platforms such as 454 and SOLiD and high-density oligo-arrays from Affymetrix and NimbelGen.
• Cost-Effective Solutions: Evaluates mixed sequencing strategies to identify cost-effective combinations that maintain high accuracy in genome reconstruction.
• Handling Complex Genome Structures: Employs mapability maps to manage the inhomogeneous, repeat-containing structure of the human genome during assembly simulations.
• Simulation of Canonical Problems: Formulates representative, computationally tractable problems that are suitable for simulation of SV reconstruction scenarios.
• Quantitative Analysis: Performs semi-realistic simulations to quantitatively compare read-length combinations and demonstrate benefits for reconstructing large novel SVs and detecting SNPs/indels.
• Enhanced Reconstruction Efficiency: Evaluates the impact of paired-end reads and the integration of arrays with sequencing on improving reconstruction efficiency for complex SVs.

Scientific Applications:

• Personal Genomics: Optimizing sequencing strategies for affordable and accurate human genome re-sequencing in personal genomics studies.
• Structural Variant Reconstruction: Assessing reconstruction and detection of large structural variants (SVs) and associated SNPs/indels in repetitive genomic regions.
• Sequencing Experimental Design: Guiding experimental design by predicting performance and cost trade-offs of mixed sequencing and array approaches.

Methodology:

Creates semi-realistic simulations using computational models to simulate combinations of sequencing technologies, employs mapability maps, formulates representative computationally tractable problems, and performs quantitative analyses.