GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists

KMC 2: fast and resource-frugal k-mer counting

(2015) Sebastian Deorowicz et al.   BIOINFORMATICS

Turtle: Identifying frequent k -mers with cache-efficient algorithms

(2014) Rajat Shuvro Roy et al.   BIOINFORMATICS

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

Strain/species identification in metagenomes using genome-specific markers

(2014) Qichao Tu et al.   NUCLEIC ACIDS RESEARCH

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

DSK: k-mer counting with very low memory usage

(2013) G. Rizk et al.   BIOINFORMATICS

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Compareads: comparing huge metagenomic experiments

(2012) Nicolas Maillet et al.   BMC BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

(2011) Eun Bae Kim et al.   NATURE

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

(2009) Stefan Kurtz et al.   BMC GENOMICS