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

# simkaMin(1)

comparative metagenomics method dedicated to NGS datasets

## NAME

simkaMin - comparative metagenomics method dedicated to NGS datasets

## DESCRIPTION

### \[main options\]:

- **-in**

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

- **-out**

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

- **-seed**

  (1 arg) :    seed used for random k-mer selection \[Default: 100\]

- **-bin**

  (1 arg) :    path to simkaMinCore program (to be specified if not in PATH, or not in standard installation directory \<simkaDir\>/build/bin/simkaMinCore)

### \[core options\]:

- **-nb-cores**

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

- **-max-memory**

  (1 arg) :    max memory (MB) \[Default: 8000\]

### \[k-mer options\]:

- **-kmer-size**

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

- **-nb-kmers**

  (1 arg) :    number of kmers used to compute distances \[Default: 1000000\]

- **-filter**

  (0 arg) :    filter out k-mer seen one time (potentially erroneous)

### \[read options\]:

- **-max-reads**

  (1 arg) :    maximum number of reads per sample to process \[Default: 0\]

- **-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 \[0,2\] \[Default: 0\]

## AUTHOR

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