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fCAT process

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Vinh Tran edited this page Nov 18, 2020 · 1 revision

fCAT algorithm consists of 3 main steps:

  1. Calculate group-specific cutoffs for a core set

Please make sure that the R dependency are available before running this function.

fcat.cutoff --coreDir /path/to/fcat_data --coreSet eukaryota
  1. Search for orthologs in a gene set of interst and create phylogenetic profiles
fcat.ortho --coreDir /path/to/fcat_data --coreSet eukaryota --refspecList "HOMSA@9606@2" --querySpecies /path/to/query.fa --annoQuery /path/to/query.json
  1. Create report for completeness assessment
fcat.report --coreDir /path/to/fcat_data --coreSet eukaryota --outDir /path/to/fcat/output --queryID queryID --mode 1

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fCAT process

R dependency

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