Annotation curation for dipteran mitogenomes

Annotation curation for dipteran mitogenomes

Usage

curate_diptera_mito(
  annotations_fn = NULL,
  assembly_fn = NULL,
  coverage_fn = NULL,
  genetic_code = 5,
  out_dir = NULL,
  max_blast_hits = 100,
  params = NULL
)

Arguments

annotations_fn

Path to the annotations file (csv)

assembly_fn

Path to the assembly file (fasta)

coverage_fn

Path to the coverage file (csv)

genetic_code

Genetic code to use (default = 2)

out_dir

Path to the output directory

max_blast_hits

Maximum number of top BLAST hits to retain (default = 100)

params

Nested list of curation parameters. Can also provided as a base64 encoded json string.