A fast and simple approach to k -mer decomposition

Alignment searches are fast heuristic methods to identify similar regions between two sequences. This group of algorithms is ubiquitously used in a myriad of software to find homologous sequences or to map sequence reads to genomes. Often the first step in alignment searches is k -mer decomposition: listing all overlapping subsequences of length k . This article presents a simple integer representation of k -mers and shows how a sequence can be quickly decomposed into k -mers in constant time with respect to k .