Looking for tools with proved accuracy to detect ploidy levels in microbial whole-genomes.
Amjad Ali sure you suggested a very important tool, but do you really understand the question? Do you understand what he asked in the question?
Ricardo Franco-Duarte It's an interesting question and with your question I came to know about the ploidy differences in microbial genomes. I have been looking at few articles and tried to understand this concept.
So, I am not giving any answer, rather, adding to your question, if someone knows the correct answer.
The ploidy level in microbial cells were observed to be changed with respect to the growth phase. So, may be there is no fixed "ploidy" in microbial cells as compared to eukaryotic cells. I have not seen any such tool, but would be good to learn about it, if there is any.
Also, what I was thinking in addition was the copy number issue. This is very common issue in many amplicon based analysis, especially 16S rRNA gene. But there is not a good method/tool available which solve this problem. So, I guess work in this direction will provide opportunities for the development of new tools which can perform such tasks.
Abhijeet Singh thanks for your input. Yes, regarding copy number there are some tools already to be applied to whole-genome data. Regarding ploidy levels, nowadays people are still using flow citometry to detect it, but I would like to know of/develop some tools to detect it using whole genomic data. I am still searching for it, and will let you know if i find out anything. Thanks again.
Ricardo Franco-Duarte Great!
If you are developing something, I would be happy to contribute for such tool.
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