kounta

Introduction

This tool will take a bunch (N) of contigs (FASTA) or reads (FASTQ.gz) and generate a tab-separated matrix with M rows and N+1 columns, where M is the number unique k-mers found across the inputs, and the columns are the k-mer string and the counts for the N genomes.

It relies on kmc for efficient k-mer counting, then uses standard Unix tools like sort, paste, cut and join to combine all the data into an output file without having to ever have it all in memory at once. The more --threads and --ram you can give it, the faster it will run, assuming your disk can keep up.

Quick Start

Using contigs

% ls *.fna
01.fna 02.fna 03.fna 04.fna

% kounta --kmer 7 --out kmers.tsv *.fna
<snip>
Done.

% head kmers.tsv
#KMER    01.fna 02.fna 03.fna 04.fna
AAAAAAA	 0      1      2      1 
AAAAAAT  1      1      1      1
AAAAAAG  3      0      0      0
AAAAATA  0      1      1      0
etc.

Using reads

% ls *q.gz
AX_R1.fq.gz BX_R1.fq.gz CX_R1.fq.gz DX_R1.fq.gz

% kounta --kmer 7 --threads 8 --ram 4 --out kmers.tsv *.fq.gz
<snip>
Done.

% head kmers.tsv
#KMER    AX_R1.fq.gz BX_R1.fq.gz CX_R1.fq.gz DX_R1.fq.gz
AAAAAAA	           0          45          21          33 
AAAAAAT           22          21          26          87
AAAAAAG           34           0           0           0
AAAAATA            0          91          76           0
etc.

Notes

Do not mix samples of reads and contigs, because the k-mer frequencies will be not comparable.
When using reads, the minimum k-mer frequency reported is --minfreq
When using reads, it is recommended to only use R1, and ignore R2 as it is normally noisier and more error-prone, and doesn't add much extra information
If you only want "core" k-mers, you can grep -v -w 0 kmers.tsv > core.tsv (NOTE: will removed header line)
To binarize the results to presence/absence you can sed -e '1 ! s/[1-9][0-9]*/1/g' kmers.tsv > yesno.tsv (NOTE: will mess up header line)

Installation

Conda

Install Conda or Miniconda:

conda install -c conda-forge -c bioconda -c defaults kounta

Homebrew

Install HomeBrew (Mac OS X) or LinuxBrew (Linux).

brew install brewsci/bio/kounta

Source

This will install the latest version direct from Github. You'll need to add the kounta bin directory to your $PATH, and also ensure all the dependencies are installed.

cd $HOME
git clone https://github.com/tseemann/kounta.git
$HOME/kounta/bin/kounta --help

Dependencies

perl >= 5.26
kmc >= 3.1
GNU parallel >= 20160101
GNU sort, paste, join, cut, uniq, wc

License

kounta is free software, released under the GPL 3.0.

Issues

Please submit suggestions and bug reports to the Issue Tracker

Author

Torsten Seemann