KCMBT

MOTIVATION: A massive number of bioinformatics applications require counting of k-length substrings in genetically important long strings. A k-mer counter generates the frequencies of each k-length substring in genome sequences. Genome assembly, repeat detection, multiple sequence alignment, error detection and many other related applications use a k-mer counter as a building block. Very fast and efficient algorithms are necessary to count k-mers in large data sets to be useful in such applications.
RESULTS: We propose a novel trie-based algorithm for this k-mer counting problem. We compare our devised algorithm k-mer Counter based on Multiple Burst Trees (KCMBT) with available all well-known algorithms. Our experimental results show that KCMBT is around 30% faster than the previous best-performing algorithm KMC2 for human genome dataset. As another example, our algorithm is around six times faster than Jellyfish2. Overall, KCMBT is 20-30% faster than KMC2 on five benchmark data sets when both the algorithms were run using multiple threads.
AVAILABILITY AND IMPLEMENTATION: KCMBT is freely available on GitHub: (https://github.com/abdullah009/kcmbt_mt).
CONTACT: rajasek@engr.uconn.edu
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

KCMBT: a k-mer Counter based on Multiple Burst Trees.

KCMBT is a trie-based algorithm for the k-mer counting problem, which is used in many bioinformatics applications. It is faster than the previous best-performing algorithm KMC2 and up to six times faster than Jellyfish2.

KCMBT

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