Frigate: a fast, in-memory tool for counting and querying k-mers.

K-mer counting is an important step in many bioinformatics applications including genome assembly, sequence error correction, and sequence alignment. As the advancements in next generation sequencing technologies have resulted in tremendous growth of genomic data, it is inevitable for k-mer counters to be faster and more efficient. We present Frigate, a fast and efficient tool capable of counting and querying k-mers. Its in-memory design utilizes multithreaded, lock-free data structures to improve performance. Frigate was developed with the emphasis on values of k less than 20, aiming to maximize performance by employing different algorithms for different ranges of k values. The results show that Frigate achieves comparable or up to 2-3x speedup compared to the state-of-the-art k-mer counters, especially for large datasets.