<tt>k</tt> <tt>mdiff</tt>, large-scale and user-friendly differential <i>k</i>-mer analyses
Téo Lemane, Rayan Chikhi, Pierre Peterlongo
Abstract
SUMMARY: Genome wide association studies elucidate links between genotypes and phenotypes. Recent studies point out the interest of conducting such experiments using k-mers as the base signal instead of single-nucleotide polymorphisms. We propose a tool, kmdiff, that performs differential k-mer analyses on large sequencing cohorts in an order of magnitude less time and memory than previously possible. AVAILABILITYAND IMPLEMENTATION: https://github.com/tlemane/kmdiff. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Topics & Concepts
Differential (mechanical device)Computer scienceBase (topology)Computational biologyScale (ratio)GenotypeGeneticsAlgorithmBioinformaticsBiologyMathematicsGenePhysicsThermodynamicsMathematical analysisQuantum mechanicsGenetic Associations and EpidemiologyBioinformatics and Genomic NetworksEpigenetics and DNA Methylation