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What's happening about my kmer spectrum? Heterozygous or repeats?
I am doing a denovo genome sequencing and i get the kmer spectrum using clean reads of two paired end libarary data(see attach files). From the plot, i see high sequencing bias and two peaks, but i can not know whether the first peak(highest) is homozygous peak or heterozygous peak, the two situation are quite different. Whether the second peak (2X peak) is from large fragment duplication? or the first peak is heterozygous peak?
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It is difficult to differentiate between zygosity effects and duplications. In part it depends on the type of organism you are sequencing. Plants are notorious for duplications but then it can be easy to breed them to be homozygous. So a bit more information would be appreciated. -
Thank you Westerman. What i am sequencing is a green algae probably diploid but we didnot have direct evidence.Originally posted by westerman View Post
From the kmer spectrum, if the first mean peak is heterozygous peak, then it is so serious. I extracted the longest scaffold and two chloroplast scaffolds from the draft assembly, it shows 1.6%,2.1%,3.1% SNP (i use a simple ciritera: base coverage>=5 and highest nuc > 80%). It is very puzzled (chloroplast SNP>nuclear genome SNP?). One paper sequenced the chloroplast genome but very fragment(the author's explanation is repeats).
Do you know why Dunaliella salina still not public one usable version from JGI? Our algae is near to Dunaliella salina from phylogenetic tree.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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