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czbiohub-sf / MIDAS

Metagenomic Intra-Species Diversity Analysis (MIDAS)
MIT License
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midas version 3 rc 1 #130

Closed zhaoc1 closed 6 months ago

zhaoc1 commented 6 months ago

Major Updates to the Pangenome Database and Profiling Methods

Pangenome:

  1. Tidy potentially incomplete ORFs;
  2. Voting mechanism for transferring annotation from ORFs to OGF (operational gene family) clusters
  3. Option prune sprurious OGF representative sequences, previously called centroid sequences. Increase the bowtie2 index without creating reference bias.
  4. Customizable for advance downstream analysis

Profiling:

  1. Improved running time for run_genes without need for cache.

TODO: the pangenome built requires much more steps, therefore the current unit test for test_db.sh is not working.