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Initialize a new project database

Source: R/init_db_userAsmb.R
new_db_userAsmb.Rd

Initialize a new project database

Usage

new_db_userAsmb(
  db_path = "./.sqlite",
  mapping_fn = NULL,
  mapping_id = "ID",
  mapping_taxon = "Taxon",
  genetic_code = NULL,
  annotate_cpus = 6,
  annotate_memory = 36,
  annotate_ref_db = "Chordata",
  annotate_ref_dir =
    "https://raw.githubusercontent.com/Smithsonian/MitoPilot/refs/heads/main/ref_dbs/Mitos2",
  mitos_opts = "--intron 0 --oril 0",
  trnaScan_opts = "-M vert -X 20",
  arwen_opts = "-mtx",
  aragorn_opts = "-m -gcstd",
  curate_cpus = 4,
  curate_memory = 8,
  curate_target = "fish_mito",
  curate_ref_db = "Metazoa_RefSeq235",
  max_blast_hits = 10,
  linear_complete = FALSE,
  curate_params = NULL,
  orf_cpus = 4,
  orf_memory = 8,
  orffinder_opts = "-s 1",
  orf_min_len = 300,
  orf_max_overlap = 0.1,
  min_assembly_length = 500
)

Arguments

db_path

Path to the new database file

mapping_fn

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

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

Optional NCBI translation table override. Default `NULL` auto-selects from the curation ruleset; a number sets an override on the default curate_opts set. https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

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

arwen_opts

Default ARWEN command line options

aragorn_opts

Default ARAGORN command line options

curate_cpus

Default # cpus for curation

curate_memory

Default memory (GB) for curation

curate_target

Default target database for curation

curate_ref_db

Default curation reference database (default = "Metazoa_RefSeq235", the only bundled DB with rRNA BLAST references)

max_blast_hits

Maximum number of top BLAST hits to retain (default = 10)

linear_complete

Treat linear assemblies as complete genomes for the export "completeness" field? By default only circular assemblies are labeled "complete genome" and linear assemblies "partial genome". Set TRUE for taxa whose complete mitogenome is genuinely linear (default = FALSE). Editable later in the curation-options modal.

curate_params

Default curation parameters

orf_cpus

CPUs for the optional ORF-finder step (default = 4)

orf_memory

Memory (GB) for the optional ORF-finder step (default = 8)

orffinder_opts

Default NCBI ORFfinder options (default = "-s 1")

orf_min_len

Minimal ORF length in nucleotides (default = 300)

orf_max_overlap

Maximum overlap with existing annotations, as a fraction of the ORF length, before an ORF is discarded (default = 0.1)

min_assembly_length

Minimum scaffold length to include in analysis (default = 500)