Efficient cardinality estimation for k-mers in large DNA sequencing data sets
preprint
OA: closed
CC-BY-4.0
AI-generated summary
This paper introduces an efficient C++ implementation with a Python interface of the HyperLogLog cardinality estimation sketch for counting DNA k-mers, distributed within the khmer software package.
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Abstract
We present an open implementation of the HyperLogLog cardinality estimation sketch for counting fixed-length substrings of DNA strings (“k-mers”). The HyperLogLog sketch implementation is in C++ with a Python interface, and is distributed as part of the khmer software package. khmer is freely available from https://github.com/dib-lab/khmer under a BSD License. The features presented here are included in version 1.4 and later.
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Source provenance
- europepmc
- last seen: 2026-05-19T01:45:01.086888+00:00
- unpaywall
- last seen: 2026-05-24T02:00:01.246996+00:00
License: CC-BY-4.0