simkaCount1

Comparative metagenomics method dedicated to ngs datasets

Overview

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']