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

# simka(1)

comparative metagenomics method dedicated to NGS datasets

## NAME

simka - comparative metagenomics method dedicated to NGS datasets

## DESCRIPTION

ERROR: Unknown parameter '-h' ERROR: Option '-in' is mandatory ERROR: Option '-out-tmp' is mandatory ERROR: Option '-in' is mandatory

\[Simka options\]

- **-in**

  (1 arg) :    input file of samples. One sample per line: id1: filename1...

- **-out**

  (1 arg) :    output directory for result files (distance matrices)  \[default './simka\_results'\]

- **-out-tmp**

  (1 arg) :    output directory for temporary files

- **-keep-tmp**

  (0 arg) :    keep temporary files

- **-data-info** (0 arg) :

  compute (and display) information before running Simka, such as the number of reads per dataset

- **-verbose**

  (1 arg) :    verbosity level  \[default '1'\]

- **-version**

  (0 arg) :    version

- **-help**

  (0 arg) :    help

-

  \[distance options\]

- **-simple-dist**

  (0 arg) :    compute all simple distances (Chord, Hellinger...)

- **-complex-dist** (0 arg) :

  compute all complex distances (Jensen-Shannon...)

-

  \[kmer options\]

- **-kmer-size**

  (1 arg) :    size of a kmer  \[default '21'\]

- **-abundance-min**

  (1 arg) :    min abundance a kmer need to be considered  \[default '2'\]

- **-abundance-max**

  (1 arg) :    max abundance a kmer can have to be considered  \[default '999999999'\]

- **-kmer-shannon-index** (1 arg) :

  minimal Shannon index a kmer should have to be kept. Float in \[0,2\]  \[default '0'\]

-

  \[read options\]

- **-max-reads**

  (1 arg) :    maximum number of reads per sample to process. Can be **-1**: use all reads. Can be 0: estimate it  \[default '-1'\]

- **-min-read-size**

  (1 arg) :    minimal size a read should have to be kept  \[default '0'\]

- **-min-shannon-index** (1 arg) :

  minimal Shannon index a read should have to be kept. Float in \[0,2\]  \[default '0'\]

-

  \[core options\]

- **-nb-cores**

  (1 arg) :    number of cores  \[default '0'\]

- **-max-memory** (1 arg) :

  max memory (MB)  \[default '5000'\]

- **-max-count**

  (1 arg) :    maximum number of simultaneous counting jobs (a higher value improve execution time but increase temporary disk usage)  \[default ''\]

- **-max-merge**

  (1 arg) :    maximum number of simultaneous merging jobs (1 job = 1 core)  \[default ''\]

-

  \[cluster options\]

- **-count-cmd**

  (1 arg) :    command to submit counting job  \[default ''\]

- **-merge-cmd**

  (1 arg) :    command to submit merging job  \[default ''\]

- **-count-file** (1 arg) :

  filename to the couting job template  \[default ''\]

- **-merge-file** (1 arg) :

  filename to the merging job template  \[default ''\]

## AUTHOR

This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.