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todo.md

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Immediate Needs for the project

  1. Modify variant_plotting.R to be interactive and to utilize a VOC file (Toby)
  2. Modify visualization to include tree (pieced back together with usher clade assignment and annotated according to cluster)
  3. Remove any specific references to FL for any regional analysis (???)
  4. Replace FastTreeMP with matUtils matOptimize (Tony)
  5. Use DeepDynaTree statistics on Oster values to assign clusters to the following categories ("Growing", "Shrinking", "Static") (BRM)

Near future for the project

  1. Alert user when/which cluster(s) have been added to, if have new mutation, and if switched Oster category (???)
  2. Better way to retrieve metadata from NCBI? (Manoj)
  3. Potentially replace viralmsa with an aligner that can handle indels and determine how to update usher info with indel data
  4. Improved molecular clock calibration (rooting is so time-consuming!), narrowing down the search for best root usng sampling dates.