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malonge / RagTag

Tools for fast and flexible genome assembly scaffolding and improvement
MIT License
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ragtag patch didn't work as expected in haplotype assembly #138

Open HippoYI opened 2 years ago

HippoYI commented 2 years ago

Hi malonge, Thanks for the useful tool. I have got three assemblies (one monoploid genome and two haplotype assemblies) of a diploid plant using HiFi+HiC. Because the haplotype assemblies had less genome size and less continuity than the monoploid genome, I want to use patch function of ragtag to fill gaps with homologous sequence of the monoploid, the command was: 

      ragtag.py patch -f 10000 --remove-small -u hap1.fa/hap2.fa monoploid.fa

 It is confused that the ragtag.patch.fasta had no change with the original hap1.fa/hap2.fa, and the program gave no errors, which means it didn't patch any sequence from the monoploid  sequences. I have tried minimap2 and nucmer, but the results were still the same. I didin't know why.

Could you help me with this and give me some hints?
Thanks so much!
Isoris commented 2 months ago

Any updates?