Home - PaleovirologyLab/hi-fever GitHub Wiki

Welcome to the hi-fever wiki! HI-FEVER is a Nextflow pipeline for finding endogenous viral elements (EVEs) in host genomes. It aims to address common issues in paleovirology including cross-matches between host proteins and EVEs, computational burden of EVE searches and incompatability between software packages or platforms. We provide HI-FEVER as an accessible and informative workflow for any EVE-discovery project.

Features

  • Protein-to-DNA based search allows detection of divergent and ancient EVEs
  • Designed to function with millions of input query proteins
  • Reconstructs the predicted EVE protein based on its closest modern match
  • Harnesses parallelisation to optimise compute resources
  • Scales from laptop to cluster
  • Conda and Docker compatible
  • LINUX, Windows and MAC compatible

HI-FEVER provides a variety of output information about candidate EVEs, suited to many downstream purposes. Outputs include:

  • Genomic coordinates of candidate EVEs
  • Closest matches in the reciprocal databases, including full taxonomical information
  • Predicted EVE protein sequences and cDNA (frameshift and premature STOP codon aware), with extension beyond original hit
  • Extracted nucleotide sequence of each candidate EVE and flanking host genome sequence
  • Metadata & statistics of the genome assemblies screened

Acknowledgements

HI-FEVER is based on the following libraries and programs directory along with their license: