---
name: "simkaCount"
section: "1"
platform: "linux"
package: "simka"
version: "1.5.3-8+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/simkaCount"
---

# simkaCount(1)

comparative metagenomics method dedicated to NGS datasets

## 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.