A kmer counting tool
kcount is a single fast kmer counting tool. It generates a kmer histogram and a database. It can merge multiple kmer databases. It is based on parallel hashing.
Either download one of the releases or git clone https://github.com/vgl-hub/kcount.git --recursive and make -j in the kcount folder.
kcount count -f input.[fasta|fastq][.gz] -k 21
It accepts multiple files as input, separated by space. To check out all options and flags use kcount -h.
You can test some typical usage with the files in the testFiles folder, e.g.:
kcount union -d testFiles/random2.kc testFiles/random2.kc -o random2.hist
This tool is part of the gfastar tool suite. If you use kcount in your work, please cite:
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristo Gallardo, Alice Giani, Olivier Fedrigo, Erich D. Jarvis