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Overview
KentUtils is a suite of tools developed at the USCS Genome Browser lab.
Using
Use the module name kentutils to discover versions available and to load the application.
Manual: To understand how an individual command works, type its name at the command line with no arguments. The resulting message will provide basic details of what the command does as well as some instructions on using it as well as a list of usable options. See the examples above.
Using
Use the module name kentutils to discover versions available and to load the application.
Example
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[]$ module load kentutils/1.04.0
[salexan5@tlog1 ~]$ axtChain
axtChain - Chain together axt alignments.
usage:
axtChain [options] -linearGap=loose in.axt tNibDir qNibDir out.chain
Where tNibDir/qNibDir are either directories full of nib files, the name
of a .2bit file, or a single fasta file with additional -faQ or -faT options.
options:
-psl Use psl instead of axt format for input
-faQ The specified qNibDir is a fasta file with multiple sequences for query
-faT The specified tNibDir is a fasta file with multiple sequences for target
NOTE: will not work with gzipped fasta files
-minScore=N Minimum score for chain, default 1000
-details=fileName Output some additional chain details
-scoreScheme=fileName Read the scoring matrix from a blastz-format file
-linearGap=<medium|loose|filename> Specify type of linearGap to use.
*Must* specify this argument to one of these choices.
loose is chicken/human linear gap costs.
medium is mouse/human linear gap costs.
Or specify a piecewise linearGap tab delimited file.
sample linearGap file (loose)
tablesize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
[salexan5@tlog1 ~]$ chainMergeSort
chainMergeSort - Combine sorted files into larger sorted file
usage:
chainMergeSort file(s)
Output goes to standard output
options:
-saveId - keep the existing chain ids.
-inputList=somefile - somefile contains list of input chain files.
-tempDir=somedir/ - somedir has space for temporary sorting data, default ./ |
This suite of tools contains over 300 individual commands:
...
Multicore
Due to this suite of tools containing over 300 individual commands, some might. The best way to check is to look at the help/usage of a particular command and see if it has options to configure threads/cores/parallel.