Jun 7, 2016

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

BioRxiv : the Preprint Server for Biology
Luiz Carlos Irber Junior, C. Titus Brown


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 \url{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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Mentioned in this Paper

Computer Software
Severe Acute Respiratory Syndrome
Medical Devices
URL Data Type
Sequence Determinations, DNA
GPER protein, human
DNA Sequence

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