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Showing content from https://github.com/lh3/minimap2/issues/484 below:

Treatment of Ambiguous Bases · Issue #484 · lh3/minimap2 · GitHub

I was hoping I could get some info from you on how Minimap2 treats ambiguous bases. I'm working on a de novo assembly project and I'm trying to better understand how the inclusion of N nucleotides between contigs, and the number of Ns included affects the mapping of those contigs and scaffolds.


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