Uses Mitos2 and tRNAscan-SE to annotate a mitogenome assembly.
Usage
annotate(
assembly_fn = NULL,
coverage_fn = NULL,
cpus = 4,
genetic_code = "2",
ref_db = "Chordata",
ref_dir = "/home/harpua/Jzonah/MitoPilot/ref_dbs/Mitos2",
mitos_opts = "--intron 0 --oril 0",
mitos_condaenv = "mitos",
trnaScan_opts = "-M vert -X 20",
trnaScan_condaenv = "base",
arwen_opts = "-mtx",
use_arwen = FALSE,
aragorn_opts = "-m -gcstd",
aragorn_condaenv = "aragorn",
use_aragorn = FALSE,
use_mitos_best = TRUE,
start_gene = "trnF",
out_dir = NULL
)Arguments
- assembly_fn
Path to the mitogenome assembly FASTA file.
- coverage_fn
Path to the mitogenome assembly coverage stats CSV file.
- cpus
Number of CPUs to use.
- genetic_code
Genetic code to use for annotation (default: 2).
- ref_db
Reference Mitos2 database to use for annotation (default: "Chordata").
- ref_dir
Path to the Mitos2 reference database.
- mitos_opts
Additional command line options for MITOS2.
- mitos_condaenv
Conda environment to run MITOS2 (default: "mitos").
- trnaScan_opts
Additional command line options for tRNAscan-SE.
- trnaScan_condaenv
Conda environment to run tRNAscan-SE (default: "base").
- arwen_opts
Additional command line options for ARWEN (default: "-mtx").
- use_arwen
logical; whether to run ARWEN tRNA prediction (default: FALSE).
- aragorn_opts
Additional command line options for ARAGORN (default: "-m -gcstd").
- aragorn_condaenv
Conda environment containing ARAGORN (default: "aragorn").
- use_aragorn
logical; whether to run ARAGORN tRNA prediction (default: FALSE).
- use_mitos_best
logical; whether to pass –best to MITOS2 (default: FALSE).
- start_gene
name of gene (PCG, rRNA, or tRNA) to start circular assembly (default = "trnF")
- out_dir
Output directory.