Mara Battagin

AlphaFamSeq is a family-based phasing algorithm that minimizes errors and maximizes allele phasing, achieving high accuracy in simulated data.

This study simulates strategies for using surrogate sire technology to enhance genetic merit in livestock breeding, finding a three-stage approach most effective for maximizing genetic gain.

The paper shows that index hopping and reference allele bias have minimal impact on genotype calls from low-coverage sequencing, but pruning low-support haplotypes introduces a significant reference allele bias.