Estimating the k-mer Coverage Frequencies in Genomic Datasets: A Comparative Assessment of the State-of-the-art

BACKGROUND: In bioinformatics, estimation of k-mer abundance histograms or just enumerat-ing the number of unique k-mers and the number of singletons are desirable in many genome sequence analysis applications. The applications include predicting genome sizes, data pre-processing for de Bruijn graph assembly methods (tune runtime parameters for analysis tools), repeat detection, sequenc-ing coverage estimation, measuring sequencing error rates, etc. Different methods for cardinality estima-tion in sequencing data have been developed in recent years. OBJECTIVE: In this article, we present a comparative assessment of the different k-mer frequency estima-tion programs (ntCard, KmerGenie, KmerStream and Khmer (abundance-dist-single.py and unique-kmers.py) to assess their relative merits and demerits. METHODS: Principally, the miscounts/error-rates of these tools are analyzed by rigorous experimental analysis for a varied range of k. We also present experimental results on runtime, scalability for larger datasets, memory, CPU utilization as well as parallelism of k-mer frequency estimation methods. RESULTS: The results indicate that ntCard is more accurate in estimating F0, f1 and full k-mer abundance histograms compared with other methods. ntCard is the fastest but it has more memory requirements compared to KmerGenie. CONCLUSION: The results of this evaluation may serve as a roadmap to potential users and practitioners of streaming algorithms for estimating k-mer coverage frequencies, to assist them in identifying an appro-priate method. Such results analysis also help researchers to discover remaining open research ques-tions, effective combinations of existing techniques and possible avenues for future research