Core Gene Sweeps phybreak_parameters.txt clarification

[rotheconrad]

Hello,

I am unclear on the parameter inputs.

What is the difference between input_contig_dir and contig_dir and how do these relate to the input genomes dir for PopCOGenT?

What are ref_iso and ref_contig supposed to be?

Thanks, Roth

[philarevalo]

I've added information on the parameters to the README which I've reproduced here. @davevanins might be able to provide more specific insights too!

ref_iso: identifier (filename without the extension) for reference genome to use for alignments. file must contain only one contig, either because it is closed or by stitching together contigs with Ns. ref_contig: sequence ID (i.e., first word in the fasta file header) of the reference genome

[Dx-wmc]

@philarevalo Hi, I think I am also a little confused about this problem. What is the difference between the two folders, input_contig_dir and contig_dir? In the README file, the knowledge mentioned that the dir needs to contain the absolute path, but did not point out the difference between the two folders and what the corresponding input genome is.