Maps a sample's reads to a reference mitogenome, feeds the consensus back in as the next mapping reference until it stops changing, then calls the published sequence from a final pass over all reads. The reference base never enters the published sequence.
Usage
map_to_ref(
id,
ref,
reads_1,
reads_2,
bowtie2_opts = "--very-sensitive-local",
consensus_opts = "-d 3 --min-BQ 20",
iter_cap = 5,
topology = NA_character_,
genetic_code = NA_integer_,
cpus = 4,
out_dir = ".",
ref_value = NA_character_,
mapper = "bowtie2"
)Arguments
- id
Sample ID.
- ref
Path to the reference (.gb or FASTA, one record).
- reads_1, reads_2
Preprocessed paired reads.
- bowtie2_opts
Flags passed verbatim to the chosen mapper.
- consensus_opts
Flags passed to samtools consensus after validation.
- iter_cap
Maximum number of iteration passes.
- topology
"circular" or "linear"; required for a FASTA reference, ignored for GenBank.
- genetic_code
The sample's genetic code, used only for a warning.
- cpus
Threads.
- out_dir
Output directory.
- ref_value
The reference exactly as the user configured it: an absolute file path, a URL, or an NCBI nucleotide accession. An accession is downloaded from GenBank here; anything else means
refis already the staged reference file.- mapper
Read mapper: "bowtie2", "bwa-mem", or "bwa-aln" (bwa aln plus sampe, for short or damaged reads such as ancient DNA). The first pass against the user's reference runs with relaxed seeding appended to the flags; later passes and the final pass use the flags as given.