Package index • MitoPilot

All functions

MitoPilot(): Open The MitoPilot GUI
add_samples(): Add samples to project database
annotate(): Mitogenome Annotation Wrapper
annotate_aragorn(): Use ARAGORN to annotate tRNAs in a mitochondrial genome assembly
annotate_arwen(): Use ARWEN to annotate tRNAs in a mitochondrial genome assembly
annotate_mitofinder(): Annotate a mitogenome assembly with MitoFinder (WF2, optional)
annotate_mitos2(): Annotate mitochondrial genomes using MITOS2
annotate_trnaScan(): Use tRNAscan-SE to annotate tRNAs in a mitochondrial genome assembly
backwards_compatibility(): Update old project database for backwards compatibility
compare_aa(): Pairwise comparison of AA sequences
compute_blast_ref_alignment(): Pre-compute a whole-genome pairwise alignment of a sample against its BLAST reference and write the result for ingestion into the blast_ref_alignment SQLite table.
coverage(): Map reads to assembly
coverage_trim(): Use coverage info to trim linear assemblies
curate_annelid_mito(): Annotation curation for annelid mitogenomes
curate_ascidiacea_mito(): Annotation curation for ascidian mitogenomes
curate_bird_mito(): Annotation curation for bird mitogenomes
curate_bivalvia_mito(): Annotation curation for bivalve mitogenomes
curate_bryozoa_mito(): Annotation curation for bryozoan mitogenomes
curate_copepod_mito(): Annotation curation for copepod mitogenomes
curate_crinoidea_mito(): Annotation curation for crinoid mitogenomes
curate_ctenophore_mito(): Annotation curation for ctenophore mitogenomes
curate_demospongiae_mito(): Annotation curation for demosponge mitogenomes
curate_diptera_mito(): Annotation curation for true fly mitogenomes
curate_echinoidea_mito(): Annotation curation for sea urchin mitogenomes
curate_fish_mito(): Annotation curation for fish mitogenomes
curate_gastropoda_mito(): Annotation curation for gastropod mitogenomes
curate_hexacoral_mito(): Annotation curation for hexacoral mitogenomes
curate_holothuroidea_mito(): Annotation curation for sea cucumber mitogenomes
curate_homoscleromorpha_mito(): Annotation curation for homoscleromorph sponge mitogenomes
curate_hydrozoa_mito(): Annotation curation for hydrozoan mitogenomes
curate_lepidosaur_mito(): Annotation curation for lepidosaur mitogenomes
curate_malacostraca_mito(): Annotation curation for malacostracan mitogenomes
curate_mammal_mito(): Annotation curation for mammal mitogenomes
curate_nemertea_mito(): Annotation curation for nemertean mitogenomes
curate_octocoral_mito(): Annotation curation for octocoral mitogenomes
curate_ophiuroidea_mito(): Annotation curation for brittle star mitogenomes
curate_platyhelminthes_mito(): Annotation curation for flatworm mitogenomes
curate_polychaeta_mito(): Annotation curation for polychaete mitogenomes
curate_pycnogonida_mito(): Annotation curation for sea spider mitogenomes
curate_sipuncula_mito(): Annotation curation for peanut worm mitogenomes
curate_starfish_mito(): Annotation curation for sea star mitogenomes
curate_thaliacea_mito(): Annotation curation for thaliacean mitogenomes
curate_thecostraca_mito(): Annotation curation for barnacle mitogenomes
curate_turtle_mito(): Annotation curation for turtle mitogenomes
custom_assembly_db(): Build custom GetOrganelle and/or MitoFinder reference databases
custom_curation_db(): Generate a custom curation database
export_db_to_csv(): Export project database to CSV
export_files(): Generate export NCBI files
fetch_blast_ref(): Fetch and parse NCBI GFF3 annotations and FASTA sequence for a BLAST top hit
fetch_blast_refs(): Fetch NCBI references for many accessions using batched EFetch requests
flag_PCG_outliers(): Flag outlier PCG annotations in an export group
generate_config(): Generate and save a reusable cluster config profile
get_assembly(): Get assembly from database
get_assembly_userAsmb(): Get assembly from database
get_top_hits_local(): Get top BLASTP hits
hydra_setup(): Configure the R session environment for the NMNH Hydra cluster
list_configs(): List available executor configs
make_PCG_alignments(): Generate HTML report woth PCG alignments
mitopilot_config_dir(): MitoPilot user config directory
new_db(): Initialize a new project database
new_db_userAsmb(): Initialize a new project database
new_project(): Initialize new MitoPilot Project
new_project_userAsmb(): Initialize new MitoPilot Project with user-provided mitogenome assemblies
new_test_project(): Initialize a test project
nextflow_cmd(): Generate Nextflow command to run pipline
orf_finder(): Find open reading frames in unannotated regions
params_annelid_mito(): Default curation and validation parameters for annelid Mitochondria
params_ascidiacea_mito(): Default curation and validation parameters for Ascidiacea mitochondria
params_bird_mito(): Default curation and validation parameters for bird Mitochondria
params_bivalvia_mito(): Default curation and validation parameters for Bivalvia mitochondria
params_bryozoa_mito(): Default curation and validation parameters for Bryozoa mitochondria
params_copepod_mito(): Default curation and validation parameters for copepod Mitochondria
params_crinoidea_mito(): Default curation and validation parameters for Crinoidea mitochondria
params_ctenophore_mito(): Default curation and validation parameters for ctenophore Mitochondria
params_demospongiae_mito(): Default curation and validation parameters for Demospongiae mitochondria
params_diptera_mito(): Default curation and validation parameters for dipteran Mitochondria
params_echinoidea_mito(): Default curation and validation parameters for Echinoidea mitochondria
params_fish_mito(): Default curation and validation parameters for Fish Mitochondria
params_gastropoda_mito(): Default curation and validation parameters for Gastropoda mitochondria
params_hexacoral_mito(): Default curation and validation parameters for hexacorals Mitochondria
params_holothuroidea_mito(): Default curation and validation parameters for Holothuroidea mitochondria
params_homoscleromorpha_mito(): Default curation and validation parameters for Homoscleromorpha mitochondria
params_hydrozoa_mito(): Default curation and validation parameters for Hydrozoa mitochondria
params_lepidosaur_mito(): Default curation and validation parameters for lepidosaur Mitochondria
params_malacostraca_mito(): Default curation and validation parameters for Malacostraca mitochondria
params_mammal_mito(): Default curation and validation parameters for mammal Mitochondria
params_nemertea_mito(): Default curation and validation parameters for Nemertea mitochondria
params_octocoral_mito(): Default curation and validation parameters for octocorals Mitochondria
params_ophiuroidea_mito(): Default curation and validation parameters for Ophiuroidea mitochondria
params_platyhelminthes_mito(): Default curation and validation parameters for Platyhelminthes mitochondria
params_polychaeta_mito(): Default curation and validation parameters for Polychaeta mitochondria
params_pycnogonida_mito(): Default curation and validation parameters for Pycnogonida mitochondria
params_sipuncula_mito(): Default curation and validation parameters for Sipuncula mitochondria
params_starfish_mito(): Default curation and validation parameters for Starfish Mitochondria
params_thaliacea_mito(): Default curation and validation parameters for Thaliacea mitochondria
params_thecostraca_mito(): Default curation and validation parameters for Thecostraca mitochondria
params_turtle_mito(): Default curation and validation parameters for turtle Mitochondria
patch_blast_ref_meta(): Re-stamp per-sample BLAST hit metadata onto a cached reference JSON
rotate_asmb(): Rotate circular mitogenome to start at given gene
ruleset_browser(): Interactive browser for MitoPilot curation rulesets
run_app(): Run the Shiny Application
run_scaffold_join(): Nextflow entry point: build + persist a joined assembly (file outputs only)
scaffold_join: Multi-scaffold assembly joining
tunnel_instructions(): Print SSH tunnel instructions for a headless GUI session
update_sample_metadata(): Update project database metadata.
update_sample_seqdata(): Update sequence files for existing project
validate_annelid_mito(): Annotation validation for annelid mitogenomes
validate_ascidiacea_mito(): Annotation validation for ascidian mitogenomes
validate_bird_mito(): Annotation validation for bird mitogenomes
validate_bivalvia_mito(): Annotation validation for bivalve mitogenomes
validate_bryozoa_mito(): Annotation validation for bryozoan mitogenomes
validate_copepod_mito(): Annotation validation for copepod mitogenomes
validate_crinoidea_mito(): Annotation validation for crinoid mitogenomes
validate_ctenophore_mito(): Annotation validation for ctenophore mitogenomes
validate_demospongiae_mito(): Annotation validation for demosponge mitogenomes
validate_diptera_mito(): Annotation validation for true fly mitogenomes
validate_echinoidea_mito(): Annotation validation for sea urchin mitogenomes
validate_fish_mito(): Annotation validation for fish mitogenomes
validate_gastropoda_mito(): Annotation validation for gastropod mitogenomes
validate_hexacoral_mito(): Annotation validation for hexacoral mitogenomes
validate_holothuroidea_mito(): Annotation validation for sea cucumber mitogenomes
validate_homoscleromorpha_mito(): Annotation validation for homoscleromorph sponge mitogenomes
validate_hydrozoa_mito(): Annotation validation for hydrozoan mitogenomes
validate_lepidosaur_mito(): Annotation validation for lepidosaur mitogenomes
validate_malacostraca_mito(): Annotation validation for malacostracan mitogenomes
validate_mammal_mito(): Annotation validation for mammal mitogenomes
validate_nemertea_mito(): Annotation validation for nemertean mitogenomes
validate_octocoral_mito(): Annotation validation for octocoral mitogenomes
validate_ophiuroidea_mito(): Annotation validation for brittle star mitogenomes
validate_platyhelminthes_mito(): Annotation validation for flatworm mitogenomes
validate_polychaeta_mito(): Annotation validation for polychaete mitogenomes
validate_pycnogonida_mito(): Annotation validation for sea spider mitogenomes
validate_sipuncula_mito(): Annotation validation for peanut worm mitogenomes
validate_starfish_mito(): Annotation validation for sea star mitogenomes
validate_thaliacea_mito(): Annotation validation for thaliacean mitogenomes
validate_thecostraca_mito(): Annotation validation for barnacle mitogenomes
validate_turtle_mito(): Annotation validation for turtle mitogenomes