Annotate mitochondrial genomes using MITOS2

Annotate mitochondrial genomes using MITOS2

Usage

annotate_mitos2(
  assembly = NULL,
  topology = "circular",
  genetic_code = "2",
  ref_db = "Chordata",
  ref_dir = "/home/harpua/Jonah/MitoPilot/ref_dbs/Mitos2",
  mitos_opts = "--best --intron 0 --oril 0",
  out = NULL,
  condaenv = "mitos"
)

Arguments

assembly

a DNAString object

topology

"circular" or "linear"

genetic_code

NCBI genetic code number (default: 2)

ref_db

Mitos2 reference database (default: "Chordata")

ref_dir

Path to Mitos2 reference database

mitos_opts

Additional command line options for MITOS2

out

output directory

condaenv

Conda environment to run MITOS2 (default: "mitos")