title: EzMap: a simple pipeline for reproducible analysis of the human virome.
abstract: CONCLUSIONS
  In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome. EzMap combines a number of tools to clean, filter, and subtract WGS reads by mapping to a reference human assembly. The relative abundance of each virus present is estimated using a maximum likelihood approach that accounts for genome size, and results are presented with interactive visualizations and taxonomy-based summaries that enable rapid insights. The pipeline is automated to run on both workstations and computing clusters for all steps. EzMap automates an otherwise tedious and time-consuming protocol and aims to facilitate rapid and reproducible insights from cfDNA.
  
  
  METHODS
  EzMap is freely available at https://github.com/dekoning-lab/ezmap.
  
  
  BACKGROUND
  jason.dekoning@ucalgary.ca.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics Bachelor of Health Sciences Program.
authors.forename: Patrick
authors.initials: P
authors.lastname: Czeczko
authors.affiliation: Department of Pediatrics, Cardiac Sciences, Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, Libin Cardiovascular Institute of Alberta.
authors.forename: Steven C
authors.initials: SC
authors.lastname: Greenway
authors.affiliation: Department of Biochemistry and Molecular Biology, Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada.
authors.forename: A P Jason
authors.initials: APJ
authors.lastname: de Koning
mesh_terms: D019295:Computational Biology / Q000379:methods; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014780:Viruses / Q000235:genetics*