supeRbaits

supeRbaits designs capture baits for targeted sequencing to support population genetics analyses of neutral and selected genomic regions using Next Generation Sequencing (NGS).

Key Features:

• Targeted Sequencing Support: Supports design of capture baits to focus Next Generation Sequencing (NGS) on specified genome segments for population genetics analyses.
• Versatile Bait Design: Generates custom bait sets from input genome sequences to accommodate species-specific target selection.
• Neutral and Selected Regions: Provides guidelines and parameters for designing baits targeting both neutral genomic regions and regions under selection.
• Implementation: Implemented as an R package with core functionality written in C++.
• Empirical Performance Evaluation: Includes evaluation of bait performance across historical and modern temporal samples.

Scientific Applications:

• Population genetics: Enables targeted capture sequencing for population genetics studies, including analyses of neutral and selected loci.
• Temporal genomic studies: Applied to historical and modern samples to assess bait performance and recover temporal genomic data.
• Species-specific evolutionary and conservation studies: Used with species such as Atlantic salmon, Atlantic cod, and tiger shark for evolutionary and conservation biology investigations.

Methodology:

The workflow applies bait-design guidelines informed by empirical research and includes evaluation of bait performance across historical and modern samples.