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Attempt to circularize a linear mitogenome assembly

Source: R/circularize_asmb.R
circularize_asmb.Rd

Many assemblers emit a circular molecule as a linear contig whose end duplicates its start. This function detects that redundant overlap by BLASTing the contig against itself, trims the duplicated copy, and (when raw reads are supplied) requires reads spanning the resulting junction before calling the assembly circular.

Usage

circularize_asmb(
  assembly_fn = NULL,
  paired_reads_1 = "NA",
  paired_reads_2 = "NA",
  min_overlap = 220,
  min_identity = 99,
  min_junction_reads = 5,
  min_overhang = 30,
  cpus = 4,
  max_contigs = 100,
  out_fn = NULL,
  log_fn = NULL,
  id = "sample",
  evidence_dir = NULL
)

Arguments

assembly_fn

Path to the input assembly (fasta)

paired_reads_1

Path to forward reads (fastq), or "NA" for none

paired_reads_2

Path to reverse reads (fastq), or "NA" for none

min_overlap

Shortest accepted self-overlap (bp, default = 220)

min_identity

Percent identity required for the overlap (default = 99)

min_junction_reads

Reads that must span the junction (default = 5)

min_overhang

Bases a read must extend past the junction on each side (default = 30)

cpus

Number of CPUs for read mapping (default = 4)

max_contigs

Most contigs an assembly may hold before the attempt is skipped altogether (default = 100). Guards a draft genome that reached this step without a mitogenome search to trim it down first.

out_fn

Path for the output fasta. When `NULL` (the default) nothing is written and the result is returned only.

log_fn

Optional path for a plain-text log

id

Sample ID, recorded in the evidence CSVs (default = "sample")

evidence_dir

Optional directory to write `circularize_overlap.csv` and `circularize_depth.csv` into

Value

(invisibly) a list with `circular` (logical, TRUE when every contig is circular), `sequence` (DNAStringSet), `trimmed` (bp removed across all contigs), `note` (human-readable summary) and `contigs`, a list of per-contig results each carrying `contig`, `circular`, `trimmed` and `note`

Details

Every contig of a fragmented assembly is attempted independently; a fragment can be a circular molecule reported linearly just as a whole assembly can.

The overlap detection follows the approach used by MitoHiFi's `circularizationCheck` (MIT licensed, Genome Research Ltd): https://github.com/marcelauliano/MitoHiFi