GED-MAP

GED-MAP maps short sequencing reads to pangenomes using elastic-degenerate strings (EDS) and minimizer indexing to represent single nucleotide polymorphisms and structural variation for accurate and efficient short-read alignment.

Key Features:

• Elastic-Degenerate String Graphs: Uses elastic-degenerate strings to encode small variations (e.g., SNPs) directly within sequences while representing larger structural variations in a graph structure, reducing graph complexity and size compared to traditional sequence graphs.
• Linearized EDS Graph Representation: Linearizes the EDS graph to enable application of conventional string mapping techniques with necessary modifications and to minimize the need to traverse graph edges during mapping.
• Minimizer Indexing: Employs a minimizer index to streamline the mapping process, improving speed and reducing memory footprint for large pangenomes such as whole human genomes.

Scientific Applications:

• Mapping bias reduction: Reduces reference bias by mapping reads to a pangenome representation rather than a single linear reference.
• Short-read mapping to pangenomes: Aligns short sequencing reads within pangenomic contexts that include SNPs and structural variation.
• Population genomics and structural-variation studies: Supports analysis of genetic diversity and structural variants in human populations.
• Evolutionary biology and personalized medicine: Facilitates studies that require accurate representation of genomic variation across individuals and populations.

Methodology:

Construct an EDS graph to represent the pangenome encoding small and structural variants, linearize the EDS graph to apply modified conventional string mapping techniques, and build a minimizer index to accelerate mapping and reduce memory usage.