Aldy 4

Aldy 4 performs star-allele calling and genotyping of pharmacogenes to determine allelic composition and copy-number variation relevant to pharmacogenomics and personalized medicine.

Key Features:

• Combinatorial Optimization: Employs combinatorial optimization techniques to achieve accurate star-allele calling across sequencing technologies.
• Support for Long Reads: Supports long-read sequencing data including Pacific Biosciences (PacBio) HiFi to resolve complex genetic variation.
• Novel Phasing Model: Incorporates a novel phasing model to improve haplotype determination within pharmacogenes.
• Improved Copy Number and Variant Calling Models: Uses enhanced models for copy number variation (CNV) calling and variant identification to improve genotyping accuracy.

Scientific Applications:

• Pharmacogenomics: Determines alleles of pharmacogenes that influence drug metabolism and response to support genotype-informed research.
• Clinical genotyping: Provides precise genotype and copy-number information to assist researchers and clinicians in developing personalized treatment plans.

Methodology:

Processes high-throughput sequencing data from whole-genome and targeted Illumina sequencing, barcoded 10x Genomics, and PacBio HiFi and integrates combinatorial optimization with copy-number calling, structural variation identification, variant calling, and phasing using a novel phasing model.