ERVsearch Documentation

• Introduction
• Prerequisites
• Installation
• Quick Start
• Pipeline Description
  • Screen
  • Classify
  • ERVRegions
• Input Files
  • Required Input Files
  • Optional Input Files
    • Custom Databases
    • Sequence List
• Databases
• Usage
  • Running the Pipeline
  • Parallelisation
  • Verbosity
• Main Output Files
  • Screen
  • Classify
  • ERVRegions
• Parameters
  • Required parameters
    • genome
    • paths
  • Optional Parameters
    • genomesplits
    • output
    • database
    • exonerate
    • usearch
    • plots
    • ORFs
    • trees
    • regions
• Functions
  • Pipeline Schematic
  • Screen
    • initiate
    • genomeToChroms
    • prepDBs
    • runExonerate
    • cleanExonerate
    • mergeOverlaps
    • makeFastas
    • renameFastas
    • makeUBLASTDb
    • runUBLASTCheck
    • classifyWithExonerate
    • getORFs
    • checkORFsUBLAST
    • assignGroups
    • summariseScreen
    • Screen
  • Classify
    • makeGroupFastas
    • makeGroupTrees
    • drawGroupTrees
    • makeSummaryFastas
    • makeSummaryTrees
    • drawSummaryTrees
    • summariseClassify
    • Classify
  • ERVRegions
    • makeCleanBeds
    • makeCleanFastas
    • findERVRegions
    • makeRegionTables
    • plotERVRegions
    • summariseERVRegions
    • ERVRegions
    • Full
• Minor Output Files
  • Screen
    • initiate
    • genomeToChroms
    • prepDBs
    • runExonerate
    • cleanExonerate
    • mergeOverlaps
    • makeFastas
    • renameFastas
    • makeUBLASTDb
    • runUBLASTCheck
    • classifyWithExonerate
    • getORFs
    • checkORFsUBLAST
    • assignGroups
    • summariseScreen
  • Classify
    • makeGroupFastas
    • makeGroupTrees
    • drawGroupTrees
    • makeSummaryFastas
    • makeSummaryTrees
    • drawSummaryTrees
    • summariseClassify
  • ERVRegions
    • makeCleanBeds
    • makeCleanFastas
    • findERVRegions
    • makeRegionTables
    • plotERVRegions
    • summariseERVRegions