MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge

Kristen J. Wade; Rayo Suseno; Kerry Kizer; Jacqueline P. Williams; Juliano André Boquett; Stacy J. Caillier; Nicholas R. Pollock; Adam Renschen; Adam Santaniello; Jorge R. Oksenberg; Paul J. Norman; Danillo G. Augusto; Jill A. Hollenbach

doi:10.1186/s13059-024-03412-6

BioinformaticsGenome biologyOct 17, 2024

Peer-reviewed journal article

MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge

Kristen J. Wade iD, Rayo Suseno iD, Kerry Kizer, Jacqueline P. Williams iD, Juliano André Boquett iD, Stacy J. Caillier iD, Nicholas R. Pollock iD, Adam Renschen iD, Adam Santaniello iD, Jorge R. Oksenberg iD, Paul J. Norman iD, Danillo G. Augusto iD, Jill A. Hollenbach iD

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Abstract

The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short read de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target-capture short read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short read data. MHConstructor facilitates wide-spread access to high quality, alignment-free MHC sequence analysis.