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cmks / DAS_Tool

DAS Tool
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[Question] Are there any parameter adjustments recommended for assemblies with both Bacteria and Eukaryotes? #44

Open jolespin opened 5 years ago

jolespin commented 5 years ago

I'm wondering if this can handle protist bins. In particular, I have an ocean dataset that I know contains a few diatoms and cyanobacteria. I would like to extract all of these. Will the marker detection toss out the Eukaryotic bins? Are there any settings you recommend for this situation?

cmks commented 5 years ago

In the current version, DAS Tool will only select for bacterial and archaeal bins. As you are also interested in cyanobacteria, I recommend first running DAS Tool and select bacterial and archaeal bins with medium to high estimated completeness (e.g. >60%). After that, I suggest running EukRep by @patrickwest on the remaining bins to identify eukaryotes.

fulaibaowang commented 3 years ago

Hi, what I though and read is to run EukRep to separate eukaryotic from prokaryotic genome before binning. If DAS tool already selectes bins using bacterial and archaea marker genes in the first place, how can there still be eukaryotes?