Efficient cardinality estimation for k-mers in large DNA sequencing data sets: k-mer cardinality estimation

Luiz C. Irber; C. Titus Brown

doi:10.1101/056846

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/khmerunder a BSD License. The features presented here are included in version 1.4 and later.

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