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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",
  mapping_geome = "GEOME_BCID",
  fetch_geome = TRUE,
  mapping_gbif = "GBIF_ID",
  fetch_gbif = TRUE,
  mapping_ncbi = "BioSample",
  fetch_ncbi = TRUE,
  link_sources = FALSE,
  genetic_code = NULL,
  dedup = FALSE,
  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/fish_mito_sampler.gb",
  mitofinder = paste("--megahit"),
  maptoref_mapper = "bowtie2",
  maptoref = .mtr_default_bowtie2,
  maptoref_consensus = .mtr_default_consensus,
  maptoref_iter = 5L,
  max_paths = 10,
  max_scaffolds = 10,
  min_assembly_length = 500,
  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
)

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)

mapping_geome

Name of the mapping-file column holding GEOME BCIDs (optional). Stored as `GEOME_BCID`. See `vignette("Specimen-Metadata")`.

fetch_geome

Fetch GEOME metadata for samples with a BCID during setup (default TRUE). Set FALSE when offline and run [fetch_geome()] later.

mapping_gbif

Name of the mapping-file column holding GBIF occurrence IDs (optional). Stored as `GBIF_ID`. See `vignette("Specimen-Metadata")`.

fetch_gbif

Fetch GBIF metadata for samples with a GBIF ID during setup (default TRUE). Set FALSE when offline and run [fetch_gbif()] later.

mapping_ncbi

Name of the mapping-file column holding NCBI BioSample or SRA accessions (optional). Must not be the sample ID column. Stored as `BioSample`. See `vignette("Specimen-Metadata")`.

fetch_ncbi

Fetch NCBI metadata for samples with a BioSample value during setup (default TRUE). Set FALSE when offline and run [fetch_ncbi()] later.

Follow links between GEOME, GBIF, and NCBI records to fill in IDs a sample does not have yet (default FALSE). Saved as the project setting. See `vignette("Specimen-Metadata")`.

genetic_code

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

dedup

Run fastp with `–dedup` to drop PCR and optical duplicates before assembly? Default FALSE keeps `–dont_eval_duplication`, the shipped fastp default. Editable later in the preprocess-options modal.

assemble_cpus

Default # cpus for assembly

assemble_memory

default memory (GB) for assembly

assembler

Assembler, choice of "GetOrganelle" (default), "MitoFinder", or "MapToRef"

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 a ten-species fish mitogenome sampler (https://raw.githubusercontent.com/Smithsonian/MitoPilot/refs/heads/main/ref_dbs/MitoFinder/fish_mito_sampler.gb)

mitofinder

Default MitoFinder command line options

maptoref_mapper

MapToRef read mapper, "bowtie2", "bwa-mem", or "bwa-aln" (default = "bowtie2")

maptoref

Default mapper options for MapToRef (default = "–very-sensitive-local")

maptoref_consensus

Default samtools consensus options for MapToRef (default = "-d 3 –min-BQ 20")

maptoref_iter

Maximum MapToRef iteration passes (default = 5)

max_paths

Maximum number of assembly paths allowed for a sample to continue past the Assemble step (default = 10). Samples exceeding this are flagged as failed and skipped by downstream steps in WF1.

max_scaffolds

Maximum number of scaffolds (within a single path) allowed for a sample to continue past the Assemble step (default = 10). Samples exceeding this are flagged as failed and skipped by downstream steps in WF1.

min_assembly_length

Minimum contig length (bp) to retain for coverage calculations, BLAST, and annotation. Scaffolds shorter than this threshold are stored but flagged as ignored (default = 500).

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)