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iqbal-lab-org / pandora

Pan-genome inference and genotyping with long noisy or short accurate reads
MIT License
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Pasting new paths back into PRG #207

Open mbhall88 opened 4 years ago

mbhall88 commented 4 years ago

@mbhall88 commented on Tue Jul 31 2018

With #29 completed, the next step is to take the new paths discovered, and put them back into the PRG. There are two ways of conceivably doing this:

  1. At runtime -> adding nodes and edges into the k-mer graph relating to the new paths.
  2. Output the paths as fasta files, redo multiple sequence alignment for that gene, rebuild PRG for that gene, redo the map step.

@mbhall88 commented on Tue Mar 05 2019

Step 2 has been successfully done. But ultimately we need to pandora to do this via step 1 - i.e automated.

bricoletc commented 4 years ago

Gramtools is also directly concerned by this