MHConstructor

MHConstructor containerizes a pipeline for high-throughput, haplotype-informed, reproducible assembly of MHC sequences from short read data, facilitating alignment-free MHC sequence analysis.

Key Features:

• Haplotype-informed assembly: Incorporates a short read de novo assembly algorithm for application to the highly polymorphic MHC region.
• Containerized pipeline: Provides a self-contained, reproducible workflow for MHC sequence assembly.
• Alignment-free analysis: Enables MHC sequence analysis without reliance on reference-based alignment methods.
• Support for multiple sequencing data types: Processes both whole genome sequencing and target-capture short read data.
• Population-scale processing: Handles large, population cohorts for high-throughput MHC assembly.

Scientific Applications:

• MHC sequence assembly: Generates de novo MHC assemblies from short read data for human population studies.
• Polymorphism analysis: Addresses the challenge of extreme genetic polymorphism within the human major histocompatibility complex that limits reference-based methods.

Methodology:

MHConstructor incorporates a short read de novo assembly algorithm into a workflow for novel application to the MHC.