kmr_scan_k_min: kmr_scan_k_min
In c5sire/kmerize: K-Mer Tools for Building Databases

Description Usage Arguments Value See Also Examples

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
)

`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

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

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

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
}