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aaranyue / quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
http://atcgn.com:8080/quarTeT/home.html
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what do the parameters "--fillonly" and "--joinonly" mean? #12

Closed hui-liu closed 11 months ago

hui-liu commented 11 months ago

Hi, I failed to understand the parameters "--fillonly" (Only fill the gaps without join) and "--joinonly" (Only join the gaps without fill), could you give me more explanation? Thanks!

Echoring commented 11 months ago

There are two ways to close a gap. "fill" means find a segment that can be placed in the gap and link them together. "join" means find an evidence that the gap edge is overlaped and can be directly merged into one. (for now, "join" is not as stable as "fill")