jlw-ecoevo / grodon Goto Github PK

Hi,

Thank you very much for developing this excellent tool.

I am particular interested in the slow growers. I generate MAGs and I found that a majority of my MAGs have minimum doubling time > 5 hours (mostly between 5 to 30), but it seems that your tool might largely underestimate the minimum doubling time if it is > 5 hours. Is it still appropriate to compare the minimum doubling time among my MAGs? The tool might underestimate, but maybe the predicted minimum doubling time is still comparable among slow-growing MAGs?

I am trying to link the MAG growth rate to their distribution pattern. It is impossible to do the analyses if I only report all my MAGs have > 5 hours. Or do you have a better idea to compare the minimum doubling time among slow growers?

Hi,

Does it make sense if I use metagenome mode for MAGs? The results I obtain from metagenome mode is in line with my expectations because the MAGs with longer doubling time tend to be dominant in nutrient-poor samples.

However, I found the results from metagenome mode is inversely related to the results from partial mode (see the figure attached). In the preprint and vignette you seem to prefer using partial mode for MAGs?
Rplot01.pdf

Hi,

Does gRodon underestimate the weighted community-level growth rate when it is larger than 5 hours?

Hi
I am really interested in your R package gRodon. I am checking the potential to use it in metagenomics data. In metagenomic mode, should I use MAGs as genome fasta input? Thanks a lot!

Best,

Hi, I have been using gRodon in the metagenome mode but want to try running the weighted option. But it is unclear to me how the median depth is calculated. I am using Prokka to annotate my metagenome assemblies. Is there a way to use the output from Prokka to calculate the read depth?

Thanks for your help!