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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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Confused about CloserScore #25

Closed Bank-tidy closed 3 months ago

Bank-tidy commented 7 months ago

Dear the author,

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, although I achieved a decent score of 1.97, the alignment results of these reads using Minimap2 and BLAST are relatively poor. Do you have any recommendations for this issue? image

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Best, Bank

Echoring commented 7 months ago

By default, quarTeT GapFiller requires >1000 bp alignment with >40% identity at both frank 5000 bp to fill the gap. Score 1.97 means the identity of the two alignments are high. In your case, I assume that the alignment is a little far from the gap. If you feel unproper, you can increase -l or decrease -f to restrict the alignment more near the gap.

Bank-tidy commented 7 months ago

@Echoring Oh, I understand, thank you for your answer!