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GWang2022 / iGDP

An integrated Genome Decontamination Pipeline for wild ciliated microeukaryotes
GNU General Public License v3.0
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telomere reads-assisted program #2

Open Zhangxp0315 opened 6 months ago

Zhangxp0315 commented 6 months ago

Hello, I have successfully completed all the example data runs now. However, I noticed that in the "telomere reads-assisted program" step, the default setting is "CCCCAA for Tetrahymena species." Does this mean that iGDP can only handle data for one species at a time in each run? If it's possible to compare telomere information for multiple species, how should I proceed? Thank you.

GWang2022 commented 6 months ago

Thank you for using iGDP.

Yes, iGDP can only separate one target species from other contaminated sequences in each run. It can not automatically identify telomere repeats for multiple species.

Actually, I am uncertain about the purpose of comparing telomere information for multiple species. Maybe you can first use binning tools, such as metabat2, to obtain several bins, and then identify the telomere repeats in each bin.

Zhangxp0315 commented 6 months ago

Thank you for your reply!