The khmer software package: enabling efficient nucleotide sequence analysis

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/ .

Cited by papers we hold 19

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• Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity · 2017
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• Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary · 2016
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• Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria · 2016
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