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can we use greyhound or MAGsearch to identify/correlate/analyze contamination?

Open ctb opened this issue 5 years ago • 1 comments

if we find suspected contamination, it would be interesting to ask --

  • does this contamination correlate in any way with the rest of the genome content, across all available metagenomes? this is in some sense a question of pairwise correlation/quilt plots, and maybe there needs to be a statistical test involved. (the searching could be done with MAGsearch)
  • what other metagenomes map to this genome, if it's a public genome? (greyhound)

ctb avatar Nov 18 '20 14:11 ctb

I think for v1, this is a bit beyond the scope of charcoal. But something to keep in mind!

ctb avatar Nov 26 '20 17:11 ctb