PGR-TK

PGR-TK performs multiscale analysis of pangenomes to represent genomic diversity and to characterize structural and haplotype variation in repetitive and clinically significant genes.

Key Features:

• Multiscale pangenome analysis: Analyzes variation across scales from tandem repeats to megabase rearrangements within pangenomes.
• Graph decomposition methodologies: Uses graph decomposition approaches to identify structural and haplotype variation within pangenomes.
• Structural and haplotype variation characterization: Detects and analyzes structural variants and haplotypes in complex genomic regions.
• Repetitive and clinically significant gene focus: Targets repetitive regions and clinically relevant loci, including tandem repeats and medically important genes.
• Integration of sequencing and assembly methods: Leverages advances in sequencing technologies and assembly methods to improve representation of genomic diversity.
• Large-scale gene applicability: Applied across 395 complex repetitive medically important genes.

Scientific Applications:

• Class II major histocompatibility complex: Analysis of the complex class II major histocompatibility complex region within the human pangenome.
• Y-chromosome DAZ genes: Analysis of structural variants in DAZ1/DAZ2/DAZ3/DAZ4 linked to male infertility.
• X-chromosome opsin genes: Examination of OPN1LW and OPN1MW variation associated with eye disorders.
• Complex medically important genes: Resolution of intricate variation across 395 complex repetitive medically important genes.

Methodology:

Applies graph decomposition methodologies to analyze structural and haplotype variation within pangenomes and leverages sequencing technologies and assembly methods.