Installation

Installation

kMate is a Python package. It also calls external programs: jellyfish (k-mer counting), samtools and bcftools.

Install

mamba create -n kmate -c conda-forge -c bioconda kmate "python<3.13"
mamba activate kmate

conda/micromamba work the same way. This pulls kMate and the programs it calls, kmer-jellyfish, samtools and bcftools.

The "python<3.13" pin matters only for kMate 0.1.4 and older, whose build-index needed jellyfish's Python bindings (bioconda ships them for Python 3.9–3.12 only; see Troubleshooting). From 0.1.5 kMate uses only the jellyfish program and runs on any Python 3.9+; the pin is harmless.

From source

To track the latest changes:

git clone https://github.com/Tatianabellagio/kMate.git
cd kMate
mamba create -n kmate -c conda-forge -c bioconda python numpy scipy pysam \
    kmer-jellyfish samtools bcftools
mamba activate kmate
pip install -e .

Check it works

kmate selftest

This runs a tiny bundled example end to end: k-mer counting, the EM, and the frequency projection.

It should end with:

PASS: kMate is correctly installed and working.

If it does not print PASS, stop and fix that first. Everything else depends on it.

Check the version

kmate --version

Use 0.1.5 or newer. 0.1.0 cannot count k-mers; 0.1.2 cannot build a panel from a Cactus pangenome without extra scripts, and its --haploidize empties haploid panels; 0.1.3 returns NaN without explanation for very-low-coverage pools; 0.1.3 and 0.1.4 need Python below 3.13 for build-index.

From source

For development, or to track the latest changes:

git clone https://github.com/Tatianabellagio/kMate.git
cd kMate
mamba create -n kmate -c conda-forge -c bioconda python numpy scipy pysam \
    kmer-jellyfish samtools bcftools
mamba activate kmate
pip install -e .
kmate selftest

What you get

kmate run             estimate frequencies for one pool
kmate build-index     build the k-mer index for a panel
kmate build-kmer-pa   build the founder x k-mer matrix
kmate build-var-pa    build the founder x variant matrix
kmate decompose       make a multi-allelic VCF biallelic
kmate build-kmer-db   count a pool's k-mers once, reuse per chromosome
kmate selftest        verify the install

Run kmate <command> --help for the options of any one of them.