Required Flags

These are the required flags that must be used during Execution. All of these commands must be used via the command line.

--runP / --runN [CMD]

  • Specify a blastp or blastx annotation
  • If - -runP is selected with a nucleotide input, frame selection will be ran and annotation stages will be executed with protein sequences (blastp)
  • If - -runP is selected with a protein input, frame selection will not be ran and annotation will be executed with protein sequences (blastp)
  • If - -runN is selected with nucleotide input, frame selection will not be ran and annotation will be executed with nucleotide sequences (blastx)

-i / --input [string] [CMD]

  • Path to the transcriptome file (either nucleotide or protein)

-d / --database [multi-string] [CMD]

  • Specify up to 5 DIAMOND indexed (.dmnd) databases to run similarity search against

--ini [string] [CMD]

  • Point to entap_config.ini to specify file paths
  • Default: entap_config.ini residing in the current working directory