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Documentation for how to use 'smasher', the taxonomy combiner. See file NEWS.md for release notes for the taxonomy itself.

Taxonomies are represented as directories, see https://github.com/OpenTreeOfLife/reference-taxonomy/wiki/Interim-taxonomy-file-format

To test to see whether you can run Smasher, do 'make aster'.

To create a new version of OTT:

  • Put previous version in tax/prev_ott/ . The taxonomy file name should be taxonomy.tsv, similarly synonyms.tsv and so on. (Around version 2.2 the file names changed from no extension to a .tsv extension.) The purpose of prev_ott is to get continuity of identifier assignments.

  • Edit definition of WHICH in Makefile to be new version number, e.g. WHICH=2.7.draft13

  • To refresh NCBI, rm -rf tax/ncbi. Similarly GBIF and Silva. (Note that GBIF is being updated very infrequently, so refreshing it is sort of a waste of time. Silva is updated every few months, I think.)

  • 'make'

  • Result will be in tax/ott/

  • Simple quality control check: do 'make short-list.tsv' - this will show you taxa have three properties: (1) are used in study OTUs, (2) are deprecated in this version of OTT 2.3, (3) have no replacement taxon id.

To make taxonomies in general:

  • Run Smasher. Command lines arguments are input taxonomies and operations to be performed. See 'nem' and 'ott' targets for examples. Taxonomy specifiers must end in /. Some operations:

    --edits

    specifies the location of directory full of edit files

    --ids / specifies a taxonomy from which identifiers will be drawn for reuse (usually the previous version of whatever it is you're building)

    --aux / force generation of preottol mapping

Taxonomies can also be specified as Newick strings (not ending in /), for testing purposes.

If you're puzzled by some decision the algorithm has made, it might be helpful to look at the log.tsv file.

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