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",
trnaScan_condaenv = "base",
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").
- start_gene
name of gene (PCG, rRNA, or tRNA) to start circular assembly (default = "trnF")
- out_dir
Output directory.