Finds the mitochondrial contigs in a whole assembly: merges the BLAST screen output, selects candidate contigs, extracts them from the assembly with `samtools faidx`, confirms them with MitoFinder, and writes the files the pipeline consumes. Called by the Assemble workflow; not intended for direct use.
Usage
find_mito(
assembly_fn = NULL,
hits_fn = NULL,
id = "sample",
mitofinder_db = NULL,
genetic_code = 2,
min_identity = 70,
min_aligned_length = 300,
min_aligned_fraction = 0.5,
max_candidates = 20,
min_genes = 3,
cpus = 4,
out_dir = "."
)Arguments
- assembly_fn
Path to the sample's full assembly (fasta)
- hits_fn
Chunk hit files written by the screen
- id
Sample ID, used to name the output fasta
- mitofinder_db
Path to a MitoFinder GenBank database, built with [custom_assembly_db()] (`db_type = "mitofinder"`)
- genetic_code
NCBI translation table passed to MitoFinder
- min_identity, min_aligned_length, min_aligned_fraction, max_candidates
Screen thresholds, see [select_mito_contigs()]
- min_genes
Mitochondrial genes a contig must carry to be confirmed
- cpus
Number of CPUs for MitoFinder
- out_dir
Directory for the outputs