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czbiohub-sf / MIDAS

Metagenomic Intra-Species Diversity Analysis (MIDAS)
MIT License
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MIDAS2 v1.1.1 major updates #124

Closed zhaoc1 closed 10 months ago

zhaoc1 commented 10 months ago

Changes to Pan-genome database:

  1. Remove centroid_99 what is short than 40% of corresponding centroid_95. Since we observed many incomplete ORFs from fragmented MAGs.
  2. We also added a functional annotation scripts, for four external tools: genomad, eggnog, refinder and mefinder.

Changes to Run-genes:

  1. We no longer compute pan-genome coverage based on centroid_99 level: we only used centroid_99 for collect reads during the competitive alignment. And computed gene coverage on the centroid_95.
  2. For the compute of mean_coverage, we used the median gene length of all the centroid_99s, for any given centroid_95.