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How could I align the gap in final assembly to the unitig graph? #765

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walt676 opened this issue Jan 23, 2025 · 2 comments
Open

How could I align the gap in final assembly to the unitig graph? #765

walt676 opened this issue Jan 23, 2025 · 2 comments

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@walt676
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walt676 commented Jan 23, 2025 •
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Hi, Thanks for this great algorithm!
I used HiFi reads and ONT UL reads to obtain assembly results by hifiasm, and used ragtag patch to close some gaps in our previous assembly results based on p_ctg.gfa results. I have two questions:

  1. I hope to locate the tangled regions of remaining gaps on the unitig graph. Do you have any suggestions?
  2. In addition, I find that there is no corresponding output file to explain how contig graph is generated according to unitig graph, and how to trace the source of part contigs in the unitig graph?
@chhylp123
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Let me upload a script for this.

@walt676
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walt676 commented Feb 10, 2025

Let me upload a script for this.

Thanks! Please let me know if it's done.

@walt676 walt676 changed the title How do I align the gap in final assembly to the unitig graph? How could I align the gap in final assembly to the unitig graph? Feb 11, 2025
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@chhylp123 @walt676