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

Autor: Wade KJ; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Suseno R; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Kizer K; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Williams J; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Boquett J; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Caillier S; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Pollock NR; Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA.; Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA., Renschen A; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Santaniello A; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Oksenberg JR; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Norman PJ; Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA.; Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA., Augusto DG; Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, USA.; Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil., Hollenbach JA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA. jill.hollenbach@ucsf.edu.; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA. jill.hollenbach@ucsf.edu.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2024 Oct 17; Vol. 25 (1), pp. 274. Date of Electronic Publication: 2024 Oct 17.
DOI: 10.1186/s13059-024-03412-6
Abstrakt: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
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