Published February 16, 2021 | Version v1.0.0
Software Open

GIGA-AnimalGenomics-BLV/PCIP: PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

Creators

  • 1. Unit of Animal Genomics, GIGA, Université de Liège (ULiège) ; Laboratory of Experimental Hematology, Institut Jules Bordet; Laboratory of Human Genetics, GIGA, Université de Liège (ULiège)
  • 2. Unit of Animal Genomics, GIGA, Université de Liège (ULiège) ; Laboratory of Experimental Hematology, Institut Jules Bordet
  • 3. HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University
  • 4. HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University; BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University
  • 5. Unit of Animal Genomics, GIGA, Université de Liège (ULiège) ; Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad
  • 6. Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes
  • 7. Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan
  • 8. Faculty of Veterinary Medicine: Ecosystem and Public Health, Calgary, AB, Canada
  • 9. Laboratory of Experimental Hematology, Institut Jules Bordet
  • 10. Department of Pathology, University Hospital (CHU), University of Liège
  • 11. Laboratory of Human Genetics, GIGA, Université de Liège (ULiège); Department of Human Genetics, University Hospital (CHU), University of Liège
  • 12. Unit of Animal Genomics, GIGA, Université de Liège (ULiège)

Description

PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

Code Release v1.0.0

Authors:

Maria Artesi; Vincent Hahaut; Basiel Cole; Laurens Lambrechts; Fereshteh Ashrafi; Ambroise Marçais; Olivier Hermine; Philip Griebel; Natasa Arsic; Frank van der Meer; Arsène Burny; Dominique Bron; Elettra Bianchi; Philippe Delvenne; Vincent Bours; Carole Charlier; Michel Georges; Linos Vandekerckhove; Anne Van den Broeke; Keith Durkin

Notes

The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV and HIV-1, endogenous retroviruses, as well as Human papillomavirus.

Files

GIGA-AnimalGenomics-BLV/PCIP-v1.0.0.zip

Files (36.4 MB)

Name Size Download all
md5:17467339f8bee9effdf7e0ab2906f18d
36.4 MB Preview Download

Additional details

Related works

Is supplement to
Software: https://github.com/GIGA-AnimalGenomics-BLV/PCIP/tree/v1.0.0 (URL)