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MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge.
Wade, Kristen J; Suseno, Rayo; Kizer, Kerry; Williams, Jacqueline; Boquett, Juliano; Caillier, Stacy; Pollock, Nicholas R; Renschen, Adam; Santaniello, Adam; Oksenberg, Jorge R; Norman, Paul J; Augusto, Danillo G; Hollenbach, Jill A.
Affiliation
  • Wade KJ; Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.
  • Suseno R; Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.
  • Kizer K; Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.
  • Williams J; Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.
  • Boquett J; Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.
  • Caillier S; Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.
  • Pollock NR; Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA.
  • Renschen A; Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA.
  • Santaniello A; Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.
  • Oksenberg JR; Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.
  • Norman PJ; Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States.
  • Augusto DG; Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA.
  • Hollenbach JA; Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA.
bioRxiv ; 2024 May 21.
Article in En | MEDLINE | ID: mdl-38826378
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: BioRxiv Year: 2024 Document type: Article Affiliation country: Estados Unidos Country of publication: Estados Unidos
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: BioRxiv Year: 2024 Document type: Article Affiliation country: Estados Unidos Country of publication: Estados Unidos