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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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How to estimate the CloserScore! #21

Closed bioinformaticspcj closed 3 months ago

bioinformaticspcj commented 8 months ago

Dear the authors,

Thank you for developing such a useful program. I have been using GapFiller to fill gaps in my genome assembly at the scaffold level. However, I found that using different lengths of the filler sequence resulted in different "CloserScores". When the CloserLength is "join", the CloserScore is "-1". I would like to know how the CloserScore is calculated and what the cut off of the CloserScore is.

Could you be kind to help me ?

Best, Bob

Echoring commented 8 months ago

When closed in fill mode, CloserScore = identity between left flank of gap and mapped sequence + identity between right flank of gap and mapped sequence. The best score is 2, the closer the more believable. When closed in join mode, CloserScore is always -1. This mode is unstable. If you want to use this mode, you'd better manually check that site. If not, use --fillonly.