ERVsearch
latest
Introduction
Prerequisites
Installation
Quick Start
Pipeline Description
Input Files
Databases
Usage
Main Output Files
Parameters
Functions
Minor Output Files
ERVsearch
»
ERVsearch Documentation
Edit on GitHub
ERVsearch Documentation
ΒΆ
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
Read the Docs
v: latest
Versions
latest
stable
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds