{{Draft}}
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 [http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads],[http://hgdownload.soe.ucsc.edu/admin/exe/],[https://github.com/ucscGenomeBrowser/kent].
=Availability and loading module =
In Compute Canada we provide all these tools through the kentutils module:
{{Commands
|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:
{{Commands
|module load gcc/5.4.0 kentutils/20180716
}}
Or
{{Commands
|module load gcc/6.4.0 kentutils/20180716
}}
Or
{{Commands
|module load gcc/7.3.0 kentutils/20180716
}}
Or
{{Commands
|module load intel/2016.4 kentutils/20180716
}}
Or
{{Commands
|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 [http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/]
=Documentation =
Issuing the command without any arguments will give a brief description of the executable in most cases.
For example:
{{Commands
|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 [http://genome.ucsc.edu/contacts.html].
=References =
[http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads Downloads]
[http://hgdownload.soe.ucsc.edu/admin/exe/ Genome Browser and Blat application binaries]
[https://github.com/ucscGenomeBrowser/kent UCSC Genome Bioinformatics Group's suite]
[http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ Executables]
[http://genome.ucsc.edu/contacts.html Discussion list]
[[Category:Bioinformatics]]
[[Category:Software]]