kmr_scan_k_min

Experimental! This function may be removed.

kmr_scan_k_min(
  a,
  b,
  k = seq(3, 13, 2),
  ci = 2,
  cx = 100,
  min_kmers = 10,
  f = "q",
  cleanup = TRUE
)

Arguments

a	sequence file path
b	sequence file path
k	k-mer size
ci	minimum cutoff; default 2
cx	maximum cutoff; default 100
min_kmers	coverage 10
f	format of files; q fastq; a fasta, m multiple fasta
cleanup	delete k-mer count files

Value

list k_min identified minimal k; table of coverage for each k

See also

Other kmer_help: kmr_compare(), kmr_length_fasta(), kmr_map_kmers(), kmr_plot_map(), kmr_plot_response(), kmr_position_coverage(), kmr_response()

Examples

if (interactive()) {
  fa <- system.file("testdata/phix174.fasta", package = "kmerize")
  a <- system.file("testdata/phix174-pe_w_err_5k_30q.fastq.gz",
                 package = "kmerize")
  b <- system.file("testdata/phix174_m-pe_w_err_5k_30q.fastq.gz",
                 package = "kmerize")

  x <- kmr_scan_k_min(a, b, k = 9, min_kmers = 3, cleanup = FALSE)
  x
}