jmcbroome / autolin

Repository containing a method for automatically identifying pathogen lineages from a phylogeny.
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Addition of LAPIS-based links and reversion columns #6

Closed jmcbroome closed 1 year ago

jmcbroome commented 1 year ago

Updates, bugfixes, and new columns representing:

  1. An immediate download of publicly-available sequences through LAPIS
  2. A download of EPI_ISLs associated with the samples in the lineage, also through LAPIS
  3. All specific reversions of mutations with respect to the parent lineage- e.g. if the parent lineage has A123G at some point in its ancestry, and the proposed child lineage has the mutation G123A, then that is tagged as a reversion. A mutation of G123C, or if A213G and G123A both occurred along the child's ancestry only and not the parent's, would not be tagged.