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Initialize a new project database

Source: R/init_db.R
new_db.Rd

Initialize a new project database

Usage

new_db(
  db_path = "./.sqlite",
  mapping_fn = NULL,
  mapping_id = "ID",
  mapping_taxon = "Taxon",
  genetic_code = 2,
  assemble_cpus = 6,
  assemble_memory = 24,
  assembler = "GetOrganelle",
  seeds_db =
    "https://raw.githubusercontent.com/smithsonian/MitoPilot/main/ref_dbs/getOrganelle/seeds/fish_mito_seeds.fasta",
  labels_db =
    "https://raw.githubusercontent.com/smithsonian/MitoPilot/main/ref_dbs/getOrganelle/labels/fish_mito_labels.fasta",
  getOrganelle = paste("-F 'anonym'", "-R 10 -k '21,45,65,85,105,115'",
    "--larger-auto-ws", "--expected-max-size 20000", "--target-genome-size 16500"),
  mitofinder_db =
    "https://raw.githubusercontent.com/Smithsonian/MitoPilot/refs/heads/main/ref_dbs/MitoFinder/NC_002333_Danio_rerio.gb",
  mitofinder = paste("--megahit"),
  annotate_cpus = 6,
  annotate_memory = 36,
  annotate_ref_db = "Chordata",
  annotate_ref_dir = "/ref_dbs/Mitos2",
  mitos_opts = "--intron 0 --oril 0",
  trnaScan_opts = "-M vert",
  curate_cpus = 4,
  curate_memory = 8,
  curate_target = "fish_mito",
  max_blast_hits = 100,
  curate_params = NULL
)

Arguments

db_path

Path to the new database file

mapping_fn

Path to the mapping CSV file. Must contain columns "ID", "Taxon, "R1", and "R2"

mapping_id

Column name of the mapping file to use as the primary key

mapping_taxon

Column name of the mapping file containing a Taxonomic identifier (eg, species name)

genetic_code

Translation table for your organisms. See NCBI website for more info https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

assemble_cpus

Default # cpus for assembly

assemble_memory

default memory (GB) for assembly

assembler

Assembler, choice of "GetOrgnalle" (default) or "MitoFinder"

seeds_db

Path to the gotOrganelle seeds database, can be a URL, cannot have same file name as labels_db. Default is a fish database built from RefSeq. https://raw.githubusercontent.com/smithsonian/MitoPilot/main/ref_dbs/getOrganelle/seeds/fish_mito_seeds.fasta

labels_db

Path to the gotOrganelle labels database, can be a URL, cannot have same file name as seeds_db. Default is a fish database built from RefSeq. https://raw.githubusercontent.com/smithsonian/MitoPilot/main/ref_dbs/getOrganelle/seeds/fish_mito_labels.fasta

getOrganelle

Default getOrganelle command line options

mitofinder_db

Path to MitoFinder reference db, must be GenBank format (.gb), can be a URL. Default is the Danio rerio mitogenome (https://raw.githubusercontent.com/Smithsonian/MitoPilot/refs/heads/main/ref_dbs/MitoFinder/NC_002333_Danio_rerio.gb)

mitofinder

Default MitoFinder command line options

annotate_cpus

Default # cpus for annotation

annotate_memory

Default memory (GB) for annotation

annotate_ref_db

Default Mitos2 reference database

annotate_ref_dir

Default Mitos2 reference database directory

mitos_opts

Default MITOS2 command line options

trnaScan_opts

Default tRNAscan-SE command line options

curate_cpus

Default # cpus for curation

curate_memory

Default memory (GB) for curation

curate_target

Default target database for curation

max_blast_hits

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

curate_params

Default curation parameters