Initialize a new project database

Usage

new_db_userAsmb(
  db_path = "./.sqlite",
  mapping_fn = NULL,
  mapping_id = "ID",
  mapping_taxon = "Taxon",
  assembly_path = NULL,
  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,
  join_scaffolds = FALSE,
  find_mitogenome = FALSE,
  mitofinder_db = NULL,
  find_min_contig_length = 500,
  find_min_identity = 70,
  find_min_aligned_length = 300,
  find_min_aligned_fraction = 0.5,
  find_max_candidates = 20,
  find_min_genes = 3,
  find_cpus = 4,
  find_memory = 8,
  attempt_circularization = FALSE,
  circularize_min_overlap = 220,
  circularize_min_identity = 99,
  circularize_min_junction_reads = 5,
  circularize_min_overhang = 30,
  circularize_cpus = 4,
  circularize_memory = 8,
  no_raw_data = FALSE
)

Arguments

db_path: Path to the new database file
mapping_fn: Path to the mapping CSV file. Must contain columns "ID", "Taxon", and "Assembly", plus "R1" and "R2" unless `no_raw_data = TRUE`. An optional "Topology" column may declare "circular" or "linear" for a single-contig assembly; blank or missing is treated as linear, and a multi-contig assembly is always recorded as "multi".
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)
assembly_path: Directory holding the user-supplied assembly files. Used to count each assembly's contigs so a multi-contig assembly is recorded with topology "multi".
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)
join_scaffolds: (logical) Order a fragmented assembly against its BLAST reference into one joined sequence during WF1 (default = FALSE). Samples whose contigs match different reference mitogenomes are left alone. So is a sample with a junction the reference cannot size, since NCBI expects the number of Ns to be the estimated gap length.
find_mitogenome: Search each user-supplied assembly for its mitochondrial contigs before the rest of WF1 runs (default = FALSE). See [find_mito()].
mitofinder_db: Path to a MitoFinder GenBank database, built with [custom_assembly_db()] (`db_type = "mitofinder"`). Required when `find_mitogenome = TRUE`.
find_min_contig_length: Contigs shorter than this are never searched, bp (default = 500)
find_min_identity: Percent identity required against the reference (default = 70)
find_min_aligned_length: Aligned bases required (default = 300)
find_min_aligned_fraction: Fraction of the contig the alignment must cover (default = 0.5). The NUMT filter.
find_max_candidates: Most contigs carried into MitoFinder confirmation (default = 20)
find_min_genes: Mitochondrial genes a contig must carry to be confirmed (default = 3)
find_cpus: Default # cpus for the search steps (default = 4)
find_memory: Default memory (GB) for the search steps (default = 8)
attempt_circularization: Try to circularize user assemblies in WF1 (default = FALSE). Each contig is attempted on its own, so a fragmented assembly is eligible; a single-contig assembly declared "circular" is skipped. See [circularize_asmb()].
circularize_min_overlap: Shortest accepted self-overlap, bp (default = 220)
circularize_min_identity: Percent identity required for the self-overlap (default = 99)
circularize_min_junction_reads: Reads that must span the new junction before an assembly is called circular (default = 5). Ignored when the project has no raw data.
circularize_min_overhang: Bases a read must extend past the junction on each side to count (default = 30)
circularize_cpus: Default # cpus for the circularization step (default = 4)
circularize_memory: Default memory (GB) for the circularization step (default = 8)
no_raw_data: (logical) Initialize a project with no raw reads (default = FALSE). When TRUE, annotation coverage trimming (`coverage_trim`) is disabled since no read-depth information is available.