Man page - simkacount(1)
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Manual
SIMKACOUNT
NAMEDESCRIPTION
AUTHOR
NAME
simkaCount - comparative metagenomics method dedicated to NGS datasets
DESCRIPTION
ERROR: Unknown parameter ’-h’ ERROR: Option ’-out-tmp-simka’ is mandatory ERROR: Option ’-bank-name’ is mandatory ERROR: Option ’-bank-index’ is mandatory ERROR: Option ’-min-read-size’ is mandatory ERROR: Option ’-min-shannon-index’ is mandatory ERROR: Option ’-max-reads’ is mandatory ERROR: Option ’-nb-datasets’ is mandatory ERROR: Option ’-nb-partitions’ is mandatory ERROR: Option ’-in’ is mandatory
[SimkaCount
options]
-nb-cores
(1 arg) : number of cores [default ’0’]
-verbose
(1 arg) : verbosity level [default ’1’]
-version
(0 arg) : version
|
-help |
(0 arg) : help |
-out-tmp-simka
(1 arg) : tmp output
-bank-name
(1 arg) : bank name
-bank-index
(1 arg) : bank name
-min-read-size
(1 arg) : bank name
-min-shannon-index
(1 arg) : bank name
-max-reads
(1 arg) : bank name
-nb-datasets
(1 arg) : bank name
-nb-partitions
(1 arg) : bank name
|
-in |
(1 arg) : reads file |
-kmer-size
(1 arg) : size of a kmer [default ’31’]
-abundance-min
(1 arg) : min abundance threshold for solid kmers [default ’0’]
-abundance-max
(1 arg) : max abundance threshold for solid kmers [default ’2147483647’]
-abundance-min-threshold
(1 arg) : min abundance hard threshold (only used when min abundance is "auto") [default ’2’]
-histo-max
(1 arg) : max number of values in kmers histogram [default ’10000’]
-solidity-kind
(1 arg) : way to compute counts of several files (sum, min, max, one, all, custom) [default ’sum’]
-solidity-custom
(1 arg) : when solidity-kind is custom, specifies list of files where kmer must be present [default ’’]
-max-memory
(1 arg) : max memory (in MBytes) [default ’5000’]
-max-disk
(1 arg) : max disk (in MBytes) [default ’0’]
-solid-kmers-out
(1 arg) : output file for solid kmers (only when constructing a graph) [default ’’]
|
-out |
(1 arg) : output file [default ’’] |
-out-dir
(1 arg) : output directory [default ’.’]
-out-tmp
(1 arg) : output directory for temporary files [default ’.’]
-out-compress
(1 arg) : h5 compression level (0:none, 9:best) [default ’0’]
-storage-type
(1 arg) : storage type of kmer counts (’hdf5’ or ’file’) [default ’hdf5’]
-histo2D
(1 arg) : compute the 2D histogram (with first file = genome, remaining files = reads) [default ’0’]
|
-histo |
(1 arg) : output the kmer abundance histogram [default ’0’] |
[kmer count, advanced performance tweaks options]
-minimizer-type
(1 arg) : minimizer type (0=lexi, 1=freq) [default ’0’]
-minimizer-size
(1 arg) : size of a minimizer [default ’10’]
-repartition-type (1 arg) :
minimizer repartition (0=unordered, 1=ordered) [default ’0’]
AUTHOR
This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.