Haploscribe

Haploscribe performs haplotype phasing from whole-genome next-generation sequencing (NGS) data of nuclear families to assign alleles to parental haplotypes and map recombination events across chromosomes.

Key Features:

• Deterministic Phasing: Employs a deterministic approach using whole-genome sequence data to assign recombinations to exact chromosomal positions and specific meiotic events.
• Comprehensive Coverage: Generates haplotypes spanning all genotyped positions, including rare variants, to phase nearly all sequenced alleles across chromosomes.
• Error Minimization: Minimizes phase misassignments (switch errors), with such errors reported as nearly absent in outputs.
• Flexibility with Family Structures: Produces multimegabase haplotypes for nuclear families with two or more children, with optimal results reported for families of four children, and can accommodate missing family members.
• Implementation as Software Scripts: The phasing algorithm is implemented as a suite of software scripts for integration into analysis workflows.

Scientific Applications:

• Personalized Medicine: Provides detailed haplotype information to inform disease risk assessment and therapeutic-response analyses at the individual level.
• Fundamental Biology: Enables study of inheritance patterns and recombination events to investigate genetic mechanisms, diversity, and evolution.

Methodology:

Analyzes whole-genome NGS data from nuclear families by determining allele phase through observed recombinations among multiple children (optimal with four children, applicable with two) and is implemented as a suite of software scripts that can handle various family configurations and missing members.