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**ebioman** · 09-05-2013, 11:21 PM

push

Actually I have no responds neither, I am afraid.
I am just asking myself the same question and wondered whether you were able to solve that question ?

**Melissa** · 09-08-2013, 09:15 AM

Perhaps you want to look into Ka/Ks estimation.

**WormSeeq** · 09-03-2015, 08:25 AM

I just came across this paper on arxiv "Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects"

Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects

http://arxiv.org/abs/1308.2012

Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often difficult to know the accurate genome size and repeat content. Furthermore, many genomes are highly repetitive or heterozygous, posing problems to current assemblers utilizing short reads. Therefore, it is necessary to develop efficient assembly-independent methods for accurate estimation of these genomic characteristics. Results: Here we present a framework for modeling the distribution of k-mer frequency from sequencing data and estimating the genomic characteristics such as genome size, repeat structure and heterozygous rate. By introducing novel techniques of k-mer individuals, float precision estimation, and proper treatment of sequencing error and coverage bias, the estimation accuracy of our method is significantly improved over existing methods. We also studied how the various genomic and sequencing characteristics affect the estimation accuracy using simulated sequencing data, and discussed the limitations on applying our method to real sequencing data. Conclusion: Based on this research, we show that the k-mer frequency analysis can be used as a general and assembly-independent method for estimating genomic characteristics, which can improve our understanding of a species genome, help design the sequencing strategy of genome projects, and guide the development of assembly algorithms. The programs developed in this research are written using C/C++, and freely accessible at Github URL (https://github.com/fanagislab/GCE) or BGI ftp ( ftp://ftp.genomics.org.cn/pub/gce).

I have not tried their tool though! It is available at ftp://ftp.genomics.org.cn/pub/gce/
Best,
~wormSeeq.

**Brian Bushnell** · 09-03-2015, 09:15 AM

Hmmm, I wrote a program that does this. Well, two, actually. Their usage is about the same.

khist.sh in=reads.fq khist=khist.txt peaks=peaks.txt
or
kmercountexact.sh in=reads.fq khist=khist.txt peaks=peaks.txt

The first uses approximate counts, while the second uses exact counts (and thus potentially more memory). The peaks file header contains estimates of genome size and heterozygousity. You can also add the flag "ploidy=2" for diploid organisms, so that it won't need to autodetect the ploidy (and thus potentially make a mistake).

These are both distributed with BBTools.

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Estimating heterozygosity from kmer frequency distribution

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