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Use tRNAscan-SE to annotate tRNAs in a mitochondrial genome assembly

Source: R/annotate_trnaScan.R
annotate_trnaScan.Rd

Use tRNAscan-SE to annotate tRNAs in a mitochondrial genome assembly

Usage

annotate_trnaScan(
  assembly = NULL,
  rotate = TRUE,
  trnaScan_opts = "-M vert -X 20",
  cpus = 4,
  out = NULL,
  condaenv = "base"
)

Arguments

assembly

a DNAStringSet of the assembly to annotate

rotate

unused; rotation now runs after tRNAscan and MITOS2 complete

trnaScan_opts

command line options for tRNAscan-SE (default = `-M vert -X 20`)

cpus

number of cpus to use (default = 4)

out

output file name

condaenv

conda environment to use (default = "base")