A pangenome refers to the complete set of genes or genetic elements found in a specific group of organisms, typically within a particular species. It represents the union of all the individual genomes within that group, including the core genome (genes shared by all individuals) and the dispensable genome (genes present in only some individuals or strains).
Pangenomics is a field of genomics that aims to capture the genetic diversity within a species by studying its pangenome. Traditional genomics focuses on analyzing and comparing the genomes of individual organisms, whereas pangenomics takes into account the genetic variation that exists across the entire species.
The concept of pangenomes is particularly relevant in species with high levels of genetic diversity, such as bacteria, viruses, plants, and some animal species. By studying the pangenome, researchers can gain insights into the genomic variations, evolutionary dynamics, and functional diversity within a species.
Pangenome analysis involves several steps, including genome sequencing and assembly of multiple individuals or strains, identification of shared and unique genes, classification of genes into core and accessory categories, and functional annotation of the genes. This analysis helps in understanding the genetic basis of phenotypic variation, adaptation, and the evolution of a species.
Pangenomics has applications in various fields, including agriculture, medicine, and evolutionary biology. It can aid in understanding host-pathogen interactions, identifying virulence factors, studying the evolution of drug resistance, and discovering new genes or pathways associated with important traits.
Overall, pangenomics provides a comprehensive perspective on the genetic diversity and complexity within a species, going beyond the analysis of individual genomes.
- human-pangenomics/hpp_pangenome_resources
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What do you want to do with pangenomes? How does that translate to a query of the pangenome?
Arya
- We would like to use the pangenome to acquire haplotypes. Our hope is that each haplotype can be used in a genome-wide association study or fine-mapping method. The approach would be to either use an existing Fine Mapping tool to identify Haplotypes and use those Haplotypes for Structural Variant Discovery or either create a workflow for tagging Haplotypes in Pangenomes
Mike
- Detect somatic structural variants with high sensitivity and specificity
- Accurately measure expression of repetitive and polymorphic transposable elements
- Build an automated workflow for benchmarking through Pangenome dataset This would involve using a leave one out approach for all genome assemblies in Pangenomes and building a graph with the rest
Would like to benchmark both of these
Aarushi
- Detect somatic structural variants with high sensitivity and specificity
- Better visualization of Pangenomes
- Benchmarking through Pangenomes
Kyle
- Visualization tool for Pangenomes
Willard