The khmer software package: enabling efficient nucleotide sequence analysis

F1000Research
Michael R CrusoeC Titus Brown

Abstract

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at  https://github.com/dib-lab/khmer/.

Associated Software

Jul 3, 2017·Cait SydneyRussell Y. Neches
Sep 21, 2015·Kevin D. MurrayScott Fay

Associated Proceedings Papers

Jul 10, 2019·Alexander LalejiniJory Schossau

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Related Concepts

Computer Software
Severe Acute Respiratory Syndrome
Replication Licensing
Medical Devices
Cocaine
Structure
Base Sequence
GPER protein, human
DNA

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