Meryl¶
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.
Publications¶
Rhie A, Walenz BP, Koren S, Phillippy AM. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology 21, 245 (2020).
Install¶
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 https://github.com/marbl/meryl.git
cd meryl/src
make -j <number of threads>
Learn¶
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