Kmer Python Packages

sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

primer-finder

Find group-specific kmers in assembled genomes to design selective (q)PCR assays

smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data

kcollections

An efficient kmer data structure for genomic applications.

biosaic

KMer level tokenizer for DNA & Proteins sequences

sqsketch

Fixed-size sketches of probability distributions: Bhattacharyya coefficient and Hellinger distance from ~1 KB per profile, with error independent of alphabet size. Library + fully verified paper (every number traced to a committed script).

pymer

Fast pythontic k-mer counting routines

stringmlst

Fast k-mer based tool for multi locus sequence typing (MLST)

kmerhash

Convert python string to hashed kmers and back again

tiptoft

Predict plasmids from uncorrected long read data

metagenomics-focus

FOCUS: An Agile Profiler for Metagenomic Data

kman

K-Mer management tools

freqgen

🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies

plasmidpredictor

Predict plasmids from uncorrected long read data