Use ARWEN to annotate tRNAs in a mitochondrial genome assembly

Use ARWEN to annotate tRNAs in a mitochondrial genome assembly

Usage

annotate_arwen(
  assembly = NULL,
  arwen_opts = "-mtx",
  genetic_code = "2",
  circular = TRUE,
  out = NULL
)

Arguments

assembly

DNAStringSet assembly to annotate

arwen_opts

command line options for ARWEN (default = "-mtx")

genetic_code

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

circular

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

out

output file path