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.
% 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.
% 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.
- 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)
conda install -c conda-forge -c bioconda -c defaults kounta
Install HomeBrew (Mac OS X) or LinuxBrew (Linux).
brew install brewsci/bio/kounta
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
perl>= 5.26kmc>= 3.1- GNU
parallel>= 20160101 - GNU
sort,paste,join,cut,uniq,wc
kounta is free software, released under the GPL 3.0.
Please submit suggestions and bug reports to the Issue Tracker
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