The khmer software package: enabling efficient nucleotide sequence analysis

By M. Crusoe, Hussien F Alameldin, Sherine Awad, E. Boucher, A. Caldwell, Reed Cartwright, Amanda L Charbonneau, B. Constantinides, Greg Edvenson, S. Fay and 51 more. F1000Research, 2015

363 citations recorded by the source corpus.

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/.

Subfields: Sociology and Political Science

View Paper: https://www.semanticscholar.org/paper/e55a332a4a2a9772add361dad6b23fd3560bc3cb

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Citations in the corpus

• Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA (2017, methodology): “For the mock community and Juday Creek samples, reads after Trimmomatic filtering were normalized based on kmer frequency (Crusoe et al., 2015) because the sequencing depth from these samples was too high.”
• Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary (2016, methodology): “Sequence data (accession number SRP039360) was downloaded from NCBI Sequence Read Archive (SRA), subsampled to coverage 50 with khmer 2.0 [30], and assembled with mismatch correction in SPAdes 3. removed by an in-house script.”