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wjian8 / psvcp_v1.01

Pan-genome Construction and Population Structure Variation Calling pipeline
GNU General Public License v3.0
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Good day! #1

Open nousiaso opened 1 year ago

nousiaso commented 1 year ago

Nice pipeline,

Wanted to ask, does the pipeline implement nucmer at the start or the user should do that? (lets say for a 5 genome comparison)

Thanks

wjian8 commented 1 year ago

The pipeline implement nucmer at the start. But the user should install MUMmer(nucmer) and add the sofeware into the environment variable before running the pepeline. In the Linux bash shell environment, you can run "nucmer -h" for testing MUMmer installation If you want to construct a linear pan-genome by 5 genome. You can put the 5 genome in the "genome_example_dir" directory, edit the "genome_list" file (see "3 Main analysis procedures") and run the code "python3 $path_of_the_pipeline/Construct_pan_and_Call_sv.py genome_example_dir genome_list "