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Nadolina / Rapid-curation-2.0

TPF-less rapid curation of genomes
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Question about dual curation #4

Open lcanesin opened 9 months ago

lcanesin commented 9 months ago

Hi Nadolina! Thanks for setting up the steps for dual curation. I am wondering if I should scaffold the haplotipic assemblies with YAHS separately before concatenating and dual curating them on PretextView. Can you point me in the right direction here?

Nadolina commented 9 months ago

Hi Lucas, no problem, I am glad to hear there are other users! Yes, our typical assembly pipeline starts with Hifiam-HiC phasing, following by scaffolding each haplotype with YAHS. Then each haplotype is decontaminated prior to concatenating them together.

lcanesin commented 9 months ago

Great! I'll do that.

Thanks again!

Rhia15 commented 6 days ago

Hi, I was also looking at the dual curation pipeline, and I think it suggests that we merge the hap1 and hap2 fasta as this image recommends:

image

I was wondering where would you scaffold these initial assemblies, would this be before or after concatenating them?

Thank you! :)

Nadolina commented 6 days ago

Hello @Rhia15 ,

You scaffold before concatenation. I am no longer in this lab space, but when I was there, the workflow was:

  1. contig assembly of hifi reads
  2. scaffold the assembly with hic
  3. decontamination
  4. curation, starting with this concatenation step