  The third-generation long reads sequencing technologies, such as PacBio and
Nanopore, have great advantages over second-generation Illumina sequencing in
de novo assembly studies. However, due to the inherent low base accuracy,
third-generation sequencing data cannot be used for k-mer counting and
estimating genomic profile based on k-mer frequencies. Thus, in current genome
projects, second-generation data is also necessary for accurately determining
genome size and other genomic characteristics. We show that corrected
third-generation data can be used to count k-mer frequencies and estimate
genome size reliably, in replacement of using second-generation data.
Therefore, future genome projects can depend on only one sequencing technology
to finish both assembly and k-mer analysis, which will largely decrease
sequencing cost in both time and money. Moreover, we present a fast
light-weight tool kmerfreq and use it to perform all the k-mer counting tasks
in this work. We have demonstrated that corrected third-generation sequencing
data can be used to estimate genome size and developed a new open-source C/C++
k-mer counting tool, kmerfreq, which is freely available at
https://github.com/fanagislab/kmerfreq.
