---
name: "simple"
section: "1"
platform: "linux"
package: "meryl"
version: "0~20150903+r2013-9+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/simple"
---

# simple(1)

the obvious array-based kmer counter

## NAME

simple - the obvious array-based kmer counter

## SYNOPSIS

**simple** \[**-f**\|**-r**\|**-C**\] \[**-c** *compression*\] \[**-m** *mersize*\] **-i** *input* **-o** *output*

## DESCRIPTION

**simple** is a very simple mer counter. It allocates a gigantic 32-bit array, populates the array with mers, sorts, and writes the output. It will allocate 4 bytes per kmer. k=16 will require 16 GB to run.

## OPTIONS

- **-i** *input*

  - **-o** *output*

  - **-m** *mersize*

  the mer size. Default is 22

- **-f**

  forward kmer (this is the default)

- **-r**

  reverse kmer

- **-C**

  canonical kmer (lexicographically smaller of the forward and reverse kmer at each location)

- **-c** *#*

  mer compression

## SEE ALSO

[**meryl**(1)](/meryl/1.md)