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Taxonomy

  • Taxonomy of a sequence is calculated at each taxonomic rank by tax-rules
  • The taxonomy of a sequence is represented by three values:
    • taxonomy : the NCBI taxonomy name at that taxonomic rank (calculated by the taxrule)
    • score : the score of the taxonomy (calculated by the taxrule)
    • c-index : count of alternative candidates for taxonomy
  • if the hits file(s) contained no hits for a given sequence or the score did not surpass --min_score FLOAT], the taxonomy is set to no-hit
  • if the taxonomy is "unresolved" (due to [--min_diff FLOAT] or two equally well scoring taxonomic names) the taxonomy is set to unresolved
  • if a taxID does not have a node at a given taxonomic rank, the taxonomy of the next highest annotated rank gets used and the suffix -undef is appended, e.g.:
    • 9823 (Sus scrofa) does not posess a node at rank "order", order is set to "Chordata-undef"
  • The taxonomy of a sequence determines its colour in a blobplot/covplot

Taxonomy