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verified publisher icon cmkobel

Report v3 progress

Open cmkobel opened this issue 2 years ago • 3 comments

Almost all is done, but some things are missing

  • [x] mlst
  • [x] abricate
  • [ ] fasttree/quicktree on core (consider skipping)
  • [ ] bakta (just copy-paste prokka)
  • [ ] eggnog (not so urgent)
  • [ ] gapseq (Should be easy, just make a heatmap of pathways)
  • [ ] antismash
  • [ ] treecluster
  • [x] dbcan results
  • [x] panaroo

cmkobel avatar Apr 05 '23 12:04 cmkobel

What about an annotation-agnostic section? Files look much the same anyway.. Just copy over the prokka one.

cmkobel avatar Aug 03 '25 17:08 cmkobel

There is no way to see the number of genes in ncbi accessions. Only via checkm but that is not from the actual annotation. An annotation agnostic one could be useful even if very simple i.e. only counting number of genes and basic stuff like that.

cmkobel avatar Sep 07 '25 21:09 cmkobel

Or maybe the info can be parsed from the downloaded ncbi annotation. I believe there is a report bundled with the download. And then that can be shown side-by-side with the bakta/prokka stats. Showing the stats that are comparable.

cmkobel avatar Sep 25 '25 10:09 cmkobel