Short variant detection with --genome option

[asan-emirsaleh]

Hello! Really good tool. Documentation is great too. But one thing is still not clear for me after I read it. What are the preferred options to perform short variant detection between two assemblies of the same genome or genomes of two close-related species? I suppose them be run-ntedit snv --reference <ref.fna> --genome <assembly2.fna> -k 55 --cutoff 1 Is it right? What is your suggestion?

[warrenlr]

Your command is correct. Note, for a higher precision, you may wish to set -j 1 -Y 1 Thank you for your interest in ntedit!