kmer2stats

kmer2stats computes k-mer based statistics for microbial community analysis, including a wide range of alpha diversity metrics (e.g. Shannon, Chao1, inverse Simpson) and descriptive count statistics (e.g. total_count, unique_kmers, percent_singletons). The output can be used for downstream plotting or comparative analyses.

Installation

All dependencies (pandas>=2.2.2, numpy>=1.26.4, scikit-bio>=0.6.3, argparse>=1.4.0) are automatically installed by both methods below.

With pip

pip install kmer2stats

Or directly from source:

git clone https://github.com/SantaMcCloud/kmer2stats.git
cd kmer2stats
pip install -r requirements.txt

With conda

conda install bioconda::kmer2stats

Usage

kmer2stats count_file

kmer2stats is also available as a Galaxy tool on the usegalaxy.eu server — search for kmer2stats in the tool panel.

Input

The input is a space-separated k-mer count file with two columns (k-mer sequence and count), without a header. This is the format produced by jellyfish dump:

AAAAAC 6870
AAAAAG 6312
AAAAAT 7966
AAAACA 5133
AAAACC 5600
AAAACG 5870
AAAACT 3911
AAAAGA 4173
AAAAGC 5078
AAAAGG 3047
AAAAGT 3067
AAAATA 5726
AAAATC 6167
AAAATG 5731
AAAATT 4987
AAACAA 3719
AAACAC 2817
AAACAG 5565
AAACAT 3342
AAACCA 5011
AAACCC 2469

A test file is provided in test_files/test_file.txt.

Output

The output is a tab-separated (TSV) file (compute_diversity.csv) with two columns: the metric name and its computed value. Diverse metrics are reported:

Richness estimators

Metric	Description
observed_features	Number of distinct k-mers observed
singles	Number of k-mers observed exactly once (singletons)
doubles	Number of k-mers observed exactly twice (doubletons)
chao1	Chao1 non-parametric richness estimator
ace	Abundance-based coverage estimator (ACE)
margalef	Margalef's richness index
menhinick	Menhinick's richness index

Diversity indices

Metric	Description
shannon	Shannon entropy (H') — measures overall diversity
brillouin_d	Brillouin index — diversity for fully censused communities
fisher_alpha	Fisher's alpha diversity index
hill	Hill number (order 1) — effective number of species
renyi	Rényi entropy
tsallis	Tsallis entropy

Evenness metrics

Metric	Description
pielou_e	Pielou's evenness (J') — Shannon evenness
heip_e	Heip's evenness index
mcintosh_e	McIntosh evenness index
simpson_e	Simpson's evenness index
enspie	ENS_PIE (effective number of species via PIE)

Dominance and concentration metrics

Metric	Description
simpson_d	Simpson's dominance index (D)
inv_simpson	Inverse Simpson index (1/D)
berger_parker_d	Berger-Parker dominance index
dominance	Dominance index
gini_index	Gini coefficient of inequality
mcintosh_d	McIntosh dominance index
strong	Strong's dominance index
kempton_taylor_q	Kempton-Taylor Q statistic

Coverage and completeness

Metric	Description
goods_coverage	Good's coverage estimator
robbins	Robbins' estimator of the probability of unseen species

Descriptive statistics

Metric	Description
total_count	Sum of all k-mer counts
unique_kmers	Number of distinct k-mers
mean_count	Mean count per k-mer
median_count	Median count per k-mer
max_count	Maximum k-mer count
min_count	Minimum k-mer count
std_count	Standard deviation of counts
count_range	Range of counts (max − min)
num_singletons	Number of k-mers with count = 1
num_doubletons	Number of k-mers with count = 2
percent_singletons	Percentage of unique k-mers that are singletons

Citation

If you use kmer2stats, please cite:

Faack, S., & Zierep, P. (2026). kmer2stats (v1.0.3). Zenodo. https://doi.org/10.5281/zenodo.19828576

License

GPL-3.0