---
name: "gmer_counter"
section: "1"
platform: "linux"
package: "genometester"
version: "4.0+git20200511.91cecb5+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmer_counter"
---

# gmer\_counter(1)

count k-mers from raw reads in FASTQ file

## NAME

gmer\_counter - count k-mers from raw reads in FASTQ file

## SYNOPSIS

**gmer\_counter** \[*OPTIONS*\] *\<SEQUENCES...\>*

## OPTIONS

**-db** DATABASE     - SNP/KMER database file

**-dbb** DBBINARY    - binary database file

**-w** FILENAME      - write binary database to file

**-32**              - use 32-bit integeres for counts (default 16-bit)

**--max\_kmers** NUM  - maximum number of kmers per node

**--header**         - print header row

**--total**          - print the total number of kmers per node

**--unique**         - print the number of nonzero kmers per node

**--kmers**          - print individual kmer counts (default if no other output)

**--compile\_index**  - Add read index to database and write it to file

**--distribution** NUM  - print kmer distribution (up to given number)

**--num\_threads**    - number of worker threads (default 24)

**--low\_memory**     - optimize for low memory usage

**-D**               - increase debug level

## EXAMPLES

 You could find some usage examples in /usr/share/doc/genometester/README.FastGT.md

## SEE ALSO

 [**glistquery**(1)](/glistquery/1.md), [**glistmaker**(1)](/glistmaker/1.md), [**glistcompare**(1)](/glistcompare/1.md), [**gmer\_caller**(1)](/gmer_caller/1.md)