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Use ARAGORN to annotate tRNAs in a mitochondrial genome assembly

Source: R/annotate_aragorn.R
annotate_aragorn.Rd

Use ARAGORN to annotate tRNAs in a mitochondrial genome assembly

Usage

annotate_aragorn(
  assembly = NULL,
  aragorn_opts = "-m -gcstd",
  genetic_code = "2",
  circular = TRUE,
  condaenv = "aragorn"
)

Arguments

assembly

DNAStringSet assembly to annotate

aragorn_opts

command line options for ARAGORN (default = "-m -gcstd")

genetic_code

NCBI translation table number passed to ARAGORN via -gc<N> (default = "2")

circular

logical; TRUE for circular topology (-c), FALSE for linear (-l)

condaenv

conda environment containing ARAGORN (default = "aragorn")