text: user12238: I have more of a conceptual question. I have two genome assemblies from the same plant, one from Dovetail technology (~998 Gb) and another is PacBio HiFi assembly (~1.1 Gb). The Dovetail assembly is more contiguous but has lower base quality whereas the PacBio has higher base quality but is more fragmented. It is a diploid organism with relatively high heterozygosity.
  I tried to use RagTag patch to improve the assembly. But no improvement was obtained.
  Is there a way to use both assemblies and produce a hybrid assembly with high contiguity and base quality?
  
  user73: Answer from @maximilian-press, converted from comment:
  I am confused when you talk about base quality, because those technologies are largely about ordering and orienting existing contigs, not assembling contigs in the first place. If you have Hi-C reads, you can read them into juicebox and actually visualize the junctions to see if the assembly makes sense: aidenlab.org/juicebox. It would also be helpful to see the actual numbers, not just "more" or "lower".
  
original_text: 12238: <p>I have more of a conceptual question. I have two genome assemblies from the same plant, one from Dovetail technology (~998 Gb) and another is PacBio HiFi assembly (~1.1 Gb). The Dovetail assembly is more contiguous but has lower base quality whereas the PacBio has higher base quality but is more fragmented. It is a diploid organism with relatively high heterozygosity.</p>
  <p>I tried to use <code>RagTag</code> <code>patch</code> to improve the assembly. But no improvement was obtained.</p>
  <p>Is there a way to use both assemblies and produce a hybrid assembly with high contiguity and base quality?</p>
   73: <p><em>Answer from @maximilian-press, converted from comment:</em></p>
  <p>I am confused when you talk about base quality, because those technologies are largely about ordering and orienting existing contigs, not assembling contigs in the first place. If you have Hi-C reads, you can read them into juicebox and actually visualize the junctions to see if the assembly makes sense: aidenlab.org/juicebox. It would also be helpful to see the actual numbers, not just &quot;more&quot; or &quot;lower&quot;.</p>
  