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manual_protocol_legacy.md

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Manual Protocol:

  1. Modify scaffold names to reflect origin haplotype (i.e./ H1.scaffold_1, H2.scaffold_1)
  2. Concatenate assemblies with modified scaffold names into a single fasta file; generate PretextMap
  3. Curate higher contiguity haplotype within haplotype combined PretextMap; paint autosomes and sex chromosomes
  4. Generate AGP from PretextView
  5. Use AGPcorrect.py to correct the scaffold sizes in the AGP that were reduced to standardized texel sizes.
python3 AGPcorrect.py <original fasta> <PrextView AGP>
  1. Separate haplotypes from corrected AGP
grep -E '#|proximity_ligation|Painted|<haplotype identifier (H1, H2)>.scaffold|<XYZW>' <corrected AGP> > main_haplotype.agp 

grep <other hap identifier (H1, H2)> > other_haplotype.agp
  1. Relocate any misphased scaffolds (see wishlist item 1)
    • create bed file of names of misphased scaffolds and pass to gfastats --exclude
    • manually edit AGPs to move scaffolds
  2. Impose corrected AGP on original fasta
gfastats <original haplotypes combined fasta> --agp-to-path <main haplotype corrected agp> -ofa
  1. Plot new PretextMap to ensure curation worked as anticipated.