zheminzhou/PEPPAN

Understanding Peppan output

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lalalagartija commented

Hi,
I wonder if there is a way to visualize your output files so that we could grasp the different stages of the analysis. I am particularily interested in the synteny.Prediction file. Is it an equivalent of what we could get from Mauve ?

Thank you very much in advance,

zheminzhou commented

Unfortunately synteny.prediction is quite different from Mauve result. It does not infer synteny blocks of genes. Instead, it is a ortholog prediction based on local synteny.

And currently there is no visualization tool for the internal results by PEPPAN. Sorry

tauqeer9 commented

Very nice tool for pangenome analysis, worked smoothly as described. Is there any script to plot rarefaction curve from "gene_content.curve" or "gene_content.Rtab" file as shown in the Fig.4 of the Genome Research paper?

Thanks

Tauqeer