BatchMap

Batchmap parallelizes construction of high-density F1 linkage maps for outcrossing species by implementing a parallelized version of the OneMap R package to process large genetic marker datasets from high-throughput sequencing.

Key Features:

• Parallelization: Parallelizes computationally intensive functions across multiple processors or nodes to accelerate genetic map construction.
• OneMap integration: Implements a parallelized modification of the OneMap R package for F1 linkage mapping in outcrossing species.
• High marker density: Optimized to handle high-density marker datasets, demonstrated up to 20,000 markers.
• Accuracy and reliability: Simulation results indicate mapping accuracy comparable to traditional methods.
• Marker density analysis: Enables exploration of the relationship between marker density and deviation from true genetic order to inform marker selection and map quality.

Scientific Applications:

• F1 linkage map construction: Construction of F1 linkage maps in outcrossing species from markers derived from high-throughput sequencing.
• Genetic architecture studies: Generation of dense linkage maps to support analyses of genetic architecture.
• Marker-assisted selection: Production of maps suitable for marker-assisted selection workflows.
• Large-scale dataset analysis: Processing of extensive HTS-derived marker datasets to enable timely genetic mapping.

Methodology:

Modifies the OneMap R package to parallelize functions that slow map construction, distributes computational tasks across multiple processors or server nodes, and uses simulations to assess accuracy and the relationship between marker density and deviation from true genetic order.