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bcgsc / ntEdit

✏️ Genome assembly polishing & SNV detection
GNU General Public License v3.0
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Short variant detection with --genome option #56

Closed asan-emirsaleh closed 4 months ago

asan-emirsaleh commented 6 months ago

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 commented 6 months ago

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!