MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge
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.
Authors
- Juliano André Boquett (ORCID: https://orcid.org/0000-0002-6437-789X)
- Adam Renschen (ORCID: https://orcid.org/0000-0002-8042-6823)
- Jill A. Hollenbach (ORCID: https://orcid.org/0000-0001-6572-7962)
- Paul J. Norman (ORCID: https://orcid.org/0000-0001-8370-7703)
- Danillo G. Augusto (ORCID: https://orcid.org/0000-0001-5665-8547)
- Kristen J. Wade (ORCID: https://orcid.org/0000-0002-0338-5028)
- Nicholas R. Pollock (ORCID: https://orcid.org/0000-0003-0114-528X)
- Stacy J. Caillier (ORCID: https://orcid.org/0000-0002-0218-2077)
- Jorge R. Oksenberg (ORCID: https://orcid.org/0000-0002-3613-9544)
- Jacqueline P. Williams (ORCID: https://orcid.org/0000-0002-5635-1526)
- Adam Santaniello (ORCID: https://orcid.org/0000-0002-9816-5932)
- Rayo Suseno
- Kerry Kizer
Institutions
- University of North Carolina at Charlotte (US)
- University of California, San Francisco (US)
- University of Colorado Anschutz Medical Campus (US)
- Universidade Federal do Paraná (BR)
Publication Details
- Journal
- Genome biology
- Published
- 2024-10-17
- DOI
- https://doi.org/10.1186/s13059-024-03412-6
- Primary Topic
- T-cell and B-cell Immunology
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Institutes of Health