Is there a program that can estimate the heterozygosity of a sample using the kmer frequency distribution of the raw reads? I have whole genome, Illumina data (100bp PE reads, from 300bp fragments). The kmer frequency plot has a clear bimodal distribution, so I can get a rough estimate by eyeballing the areas under the curves for the two peaks. I am hoping to find a more robust method and more automated since I have over 100 samples.
Seqanswers Leaderboard Ad
Collapse
X
-
I just came across this paper on arxiv "Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects"
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.
Comment
-
-
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.
Comment
-
Latest Articles
Collapse
-
by seqadmin
The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...-
Channel: Articles
03-24-2025, 11:48 AM -
-
by seqadmin
This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.
The Headliner
The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...-
Channel: Articles
03-03-2025, 01:39 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 03-20-2025, 05:03 AM
|
0 responses
49 views
0 reactions
|
Last Post
by seqadmin
03-20-2025, 05:03 AM
|
||
Started by seqadmin, 03-19-2025, 07:27 AM
|
0 responses
57 views
0 reactions
|
Last Post
by seqadmin
03-19-2025, 07:27 AM
|
||
Started by seqadmin, 03-18-2025, 12:50 PM
|
0 responses
49 views
0 reactions
|
Last Post
by seqadmin
03-18-2025, 12:50 PM
|
||
Started by seqadmin, 03-03-2025, 01:15 PM
|
0 responses
200 views
0 reactions
|
Last Post
by seqadmin
03-03-2025, 01:15 PM
|
Comment