Hi there,
I've used jellyfish kmer count to estimate the genome size of a diploid organism. I get double peaks, which are expected, and the first one is twice the size, which is also expected when sequencing diploid. However, I've always been told the protocol is to disregard the first one, as it represents the heterozygous alleles, and use the peak of the second one for genome size estimation. But this advice has mainly been for haploid sequencing.
And this paper, https://academic.oup.com/dnaresearch...inbred-line-of, looking at a tetraploid, used the first peak in their estimation.
Would I be justified in using the first peak for estimation of a diploid genome? I can't think why I wouldn't, but don't want to have overlooked something critical.
For what it's worth, when using the first peak, I get an estimation of 170 Mbp, which is around the right size (same as sister-species), and when using SOAPdenovo and Abyss to assemble, I get an assembly twice that at 330-340 Mbp. I'm assuming that the assemblers aren't handling the diploidy overly well. So, as an aside, does anyone have any advice on making the assemblers incorporate the heterozygosity of a diploid genome?
Cheers
I've used jellyfish kmer count to estimate the genome size of a diploid organism. I get double peaks, which are expected, and the first one is twice the size, which is also expected when sequencing diploid. However, I've always been told the protocol is to disregard the first one, as it represents the heterozygous alleles, and use the peak of the second one for genome size estimation. But this advice has mainly been for haploid sequencing.
And this paper, https://academic.oup.com/dnaresearch...inbred-line-of, looking at a tetraploid, used the first peak in their estimation.
Would I be justified in using the first peak for estimation of a diploid genome? I can't think why I wouldn't, but don't want to have overlooked something critical.
For what it's worth, when using the first peak, I get an estimation of 170 Mbp, which is around the right size (same as sister-species), and when using SOAPdenovo and Abyss to assemble, I get an assembly twice that at 330-340 Mbp. I'm assuming that the assemblers aren't handling the diploidy overly well. So, as an aside, does anyone have any advice on making the assemblers incorporate the heterozygosity of a diploid genome?
Cheers
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