ERVsearch
  • Introduction
  • Prerequisites
  • Installation
  • Quick Start
  • Pipeline Description
  • Input Files
  • Databases
  • Usage
  • Main Output Files
  • Parameters
  • Functions
  • Minor Output Files
ERVsearch
  • »
  • ERVsearch Documentation
  • View page source

ERVsearch DocumentationΒΆ

  • 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

© Copyright 2020, Katy Brown

Built with Sphinx using a theme provided by Read the Docs.