Meryl is a tool for working with sets of kmers. A set of kmers, when annotated with an integer value (typically the number of times the kmer occurs in a set of sequences) and optionally a label, is termed a database. Meryl comprises three (modules), one for generating kmer databases, one for filtering and combining databases, and one for searching databases. A simple, but yet to be documented, C++ API to access kmer databases exists.


Rhie A, Walenz BP, Koren S, Phillippy AM. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology 21, 245 (2020).


The easiest way to get started is to download a release. If you encounter any issues, please report them using the github issues page.

Alternatively, you can also build the latest unreleased from github:

git clone
cd meryl/src
make -j <number of threads>


NOTE! This documentation applies to meryl2. The original meryl is quite similar, but doesn’t support filters or labels, and the specification of actions is much simpler.

  • Quick Start - no experience or data required, download and analyze Escherichia coli repeats today!

  • Usage - command line usage cheat sheet

  • Reference - all the details

  • History - the history of meryl

  • FAQ - Frequently asked questions