Count K-mers in FASTQ Files

We are using simulated k-mer data from the phi-X174 genome.

Getting the data and setting parameters:

suppressPackageStartupMessages(
  library(kmerize)
)


fq <- system.file("testdata/phix174-pe_w_err_5k_30q.fastq.gz",
                  package = "kmerize")
k <- 9

out_file <- file.path(tempdir(), "phwei11")
out_db <- paste0(out_file, c(".kmc_pre", ".kmc_suf"))

Counting:

if (kmerize:::check_install_ok()) {
kmer_path = kmr_count(fq, out_file,
                  k = k,
                  f = "q" # file input format is fastq
                  )
}

Convert to readable tabulated database:

if (kmerize:::check_install_ok()) {
kp <- kmr_write_tab(kmer_path)

kmers <- kmr_read_tab(kp)
head(kmers)
}
#> # A tibble: 6 x 2
#>   kmer      count
#>   <chr>     <dbl>
#> 1 AAAAAAAGT    27
#> 2 AAAAAACGT    37
#> 3 AAAAAAGCC    38
#> 4 AAAAAAGTT    27
#> 5 AAAAAATTT    52
#> 6 AAAAACATT    25

Genomic Response

# Getting the DNA
if (kmerize:::check_install_ok()) {
fp <- system.file("testdata/phix174.fasta",
                  package = "kmerize")
dna <- Biostrings::readDNAStringSet(fp)

k <- as.integer(seq(3, 25, 2)) # currently k explicitly as integer sequence
res <- kmr_response(fp, k, fmt = "m")
res
}
#> =====
#>    k unique distinct total universe
#> 1  3      0       32  5328       32
#> 2  5     10      506  5382      512
#> 3  7   2295     3547  5380     8192
#> 4  9   4972     5170  5378   131072
#> 5 11   5346     5361  5376  2097152
#> 6 13   5374     5374  5374 33554432

if (kmerize:::check_install_ok()) {

kmr_plot_response(res, ref_k = 9, max_y = Biostrings::width(dna))
}

Basic

Count K-mers in FASTQ Files

Genomic Response