This site replaces the former Compute Canada documentation site, and is now being managed by the Digital Research Alliance of Canada.

Ce site remplace l'ancien site de documentation de Calcul Canada et est maintenant géré par l'Alliance de recherche numérique du Canada.

This article is a draft

This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.

KentUtils are the UCSC Genome Bioinformatics Group's suite of biological analysis and web display programs as well as some of Jim Kent's own tools [1],[2],[3].

Availability and loading module

In Compute Canada we provide all these tools through the kentutils module:

[name@server ~]$ module spider kentutils/20180716

Which should give you the usual prerequisites:

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  kentutils: kentutils/20180716
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
    Description:
      Kent utilities: collection of tools used by the UCSC genome browser.

    Properties:
      Bioinformatic libraries/apps / Logiciels de bioinformatique

    You will need to load all module(s) on any one of the lines below before the "kentutils/20180716" module is available to load.

      nixpkgs/16.09  gcc/5.4.0
      nixpkgs/16.09  gcc/6.4.0
      nixpkgs/16.09  gcc/7.3.0
      nixpkgs/16.09  intel/2016.4
      nixpkgs/16.09  intel/2018.3
 
    Help:
      
      Description
      ===========
      Kent utilities: collection of tools used by the UCSC genome browser.
      
      
      More information
      ================
       - Homepage: http://genome.cse.ucsc.edu/

To load, simply load the prerequisites before or along with the package:

[name@server ~]$ module load gcc/5.4.0 kentutils/20180716

Or

[name@server ~]$ module load gcc/6.4.0 kentutils/20180716

Or

[name@server ~]$ module load gcc/7.3.0 kentutils/20180716

Or

[name@server ~]$ module load intel/2016.4 kentutils/20180716

Or

[name@server ~]$ module load intel/2018.3 kentutils/20180716

The availability of different pre-requisites allow you to load other modules that you might need in your pipeline without affecting the KentUtils load.

Tools available

Kentutils provides the following tools:

addCols
ameme
autoDtd
autoSql
autoXml
ave
aveCols
axtChain
axtSort
axtSwap
axtToMaf
axtToPsl
bamToPsl
barChartMaxLimit
bedClip
bedCommonRegions
bedCoverage
bedExtendRanges
bedGeneParts
bedGraphPack
bedGraphToBigWig
bedIntersect
bedItemOverlapCount
bedJoinTabOffset
bedJoinTabOffset.py
bedMergeAdjacent
bedPartition
bedPileUps
bedRemoveOverlap
bedRestrictToPositions
bedSort
bedToBigBed
bedToExons
bedToGenePred
bedToPsl
bedWeedOverlapping
bigBedInfo
bigBedNamedItems
bigBedSummary
bigBedToBed
bigMafToMaf
bigPslToPsl
bigWigAverageOverBed
bigWigCat
bigWigCluster
bigWigCorrelate
bigWigInfo
bigWigMerge
bigWigSummary
bigWigToBedGraph
bigWigToWig
binFromRange
blastToPsl
blastXmlToPsl
blat
calc
catDir
catUncomment
chainAntiRepeat
chainBridge
chainFilter
chainMergeSort
chainNet
chainPreNet
chainSort
chainSplit
chainStitchId
chainSwap
chainToAxt
chainToPsl
chainToPslBasic
checkAgpAndFa
checkCoverageGaps
checkHgFindSpec
checkTableCoords
chopFaLines
chromGraphFromBin
chromGraphToBin
chromToUcsc
clusterGenes
colTransform
countChars
cpg_lh
crTreeIndexBed
crTreeSearchBed
dbSnoop
dbTrash
endsInLf
estOrient
expMatrixToBarchartBed
faAlign
faCmp
faCount
faFilter
faFilterN
faFrag
faNoise
faOneRecord
faPolyASizes
faRandomize
faRc
faSize
faSomeRecords
faSplit
faToFastq
faToTab
faToTwoBit
faTrans
fastqStatsAndSubsample
fastqToFa
featureBits
fetchChromSizes
findMotif
fixStepToBedGraph.pl
gapToLift
genePredCheck
genePredFilter
genePredHisto
genePredSingleCover
genePredToBed
genePredToBigGenePred
genePredToFakePsl
genePredToGtf
genePredToMafFrames
genePredToProt
gensub2
getRna
getRnaPred
gff3ToGenePred
gff3ToPsl
gmtime
gtfToGenePred
headRest
hgBbiDbLink
hgFakeAgp
hgFindSpec
hgGcPercent
hgGoldGapGl
hgLoadBed
hgLoadChain
hgLoadGap
hgLoadMaf
hgLoadMafSummary
hgLoadNet
hgLoadOut
hgLoadOutJoined
hgLoadSqlTab
hgLoadWiggle
hgSpeciesRna
hgTrackDb
hgWiggle
hgsql
hgsqldump
hgvsToVcf
hicInfo
htmlCheck
hubCheck
hubClone
hubPublicCheck
ixIxx
lastz-1.04.00
lastz_D-1.04.00
lavToAxt
lavToPsl
ldHgGene
liftOver
liftOverMerge
liftUp
linesToRa
localtime
mafAddIRows
mafAddQRows
mafCoverage
mafFetch
mafFilter
mafFrag
mafFrags
mafGene
mafMeFirst
mafNoAlign
mafOrder
mafRanges
mafSpeciesList
mafSpeciesSubset
mafSplit
mafSplitPos
mafToAxt
mafToBigMaf
mafToPsl
mafToSnpBed
mafsInRegion
makeTableList
maskOutFa
mktime
mrnaToGene
netChainSubset
netClass
netFilter
netSplit
netSyntenic
netToAxt
netToBed
newProg
newPythonProg
nibFrag
nibSize
oligoMatch
overlapSelect
para
paraFetch
paraHub
paraHubStop
paraNode
paraNodeStart
paraNodeStatus
paraNodeStop
paraSync
paraTestJob
parasol
positionalTblCheck
pslCDnaFilter
pslCat
pslCheck
pslDropOverlap
pslFilter
pslHisto
pslLiftSubrangeBlat
pslMap
pslMapPostChain
pslMrnaCover
pslPairs
pslPartition
pslPosTarget
pslPretty
pslRc
pslRecalcMatch
pslRemoveFrameShifts
pslReps
pslScore
pslSelect
pslSomeRecords
pslSort
pslStats
pslSwap
pslToBed
pslToBigPsl
pslToChain
pslToPslx
pslxToFa
qaToQac
qacAgpLift
qacToQa
qacToWig
raSqlQuery
raToLines
raToTab
randomLines
rmFaDups
rowsToCols
sizeof
spacedToTab
splitFile
splitFileByColumn
sqlToXml
strexCalc
stringify
subChar
subColumn
tabQuery
tailLines
tdbQuery
tdbRename
tdbSort
textHistogram
tickToDate
toLower
toUpper
trackDbIndexBb
transMapPslToGenePred
trfBig
twoBitDup
twoBitInfo
twoBitMask
twoBitToFa
ucscApiClient
udr
vai.pl
validateFiles
validateManifest
varStepToBedGraph.pl
webSync
wigCorrelate
wigEncode
wigToBigWig
wordLine
xmlCat
xmlToSql

Versions

The latest version of KentUtils tools in the software stack was released in April 2018 [4]

Documentation

Issuing the command without any arguments will give a brief description of the executable in most cases.

For example:

[name@server ~]$ gtfToGenePred

Will result in:

gtfToGenePred - convert a GTF file to a genePred
usage:
   gtfToGenePred gtf genePred

options:
     -genePredExt - create a extended genePred, including frame
      information and gene name
     -allErrors - skip groups with errors rather than aborting.
      Useful for getting infomation about as many errors as possible.
     -ignoreGroupsWithoutExons - skip groups contain no exons rather than
      generate an error.
     -infoOut=file - write a file with information on each transcript
     -sourcePrefix=pre - only process entries where the source name has the
      specified prefix.  May be repeated.
     -impliedStopAfterCds - implied stop codon in after CDS
     -simple    - just check column validity, not hierarchy, resulting genePred may be damaged
     -geneNameAsName2 - if specified, use gene_name for the name2 field
      instead of gene_id.
     -includeVersion - it gene_version and/or transcript_version attributes exist, include the version
      in the corresponding identifiers.

Many of the KentUtils executables are poorly documented. If you require specific help about the executables, you can submit questions to the main UCSC discussion list. See [5].