table of contents
| SIMKACOUNT(1) | User Commands | SIMKACOUNT(1) |
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.
| September 2019 | simkaCount 1.5.1 |