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

# simkaMin\_update(1)

comparative metagenomics method dedicated to NGS datasets

## NAME

simkaMin\_update - comparative metagenomics method dedicated to NGS datasets

## DESCRIPTION

### \[main options\]:

- **-in**

  (1 arg) :    input file of datasets (datasets to add to existing simka results

- **-in-to-update**

  (1 arg) :    path to existing simka results to update (existing results will be overwritten)

- **-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) \[Default: 8000\]

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

- **-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.