Summarise the reads for indel and GC content and produce the read depth plot

Source: R/summary_reads.R

Still in dev, but work nicely. Summarise the reads for indel and GC content and produce the read depth plot

summary_reads(
  fq.files,
  paired.end = FALSE,
  output = "08_stacks_results/02_summary_reads",
  read.depth.plot = TRUE,
  min.coverage.fig = 7L,
  parallel.core = parallel::detectCores() - 1
)

Arguments

fq.files

(character, path) The path to the individual fastq file to check, or the entire fq folder.

paired.end

(logical) Are the files paired-end. Default: paired.end = FALSE.

output

(path) Write the output in a specific directory. Default: output = "08_stacks_results/02_summary_reads".

read.depth.plot

(logical) To get the interesting summaries on the read content, the function is very close to similar to read_depth_plot, so you can produce it for each sample with minimal cost on time. Default: read.depth.plot = TRUE.

min.coverage.fig

(integer). Minimum coverage used to draw the color on the figure. Default: min.coverage.fig = 7L.

parallel.core

(integer) Enable parallel execution with the number of threads. Default: parallel.core = parallel::detectCores() - 1.

Value

The function returns the read depth groups plot and the read stats overall and by read depth groups.

Examples

if (FALSE) { # \dontrun{
require(vroom)
sum <- summary_reads(fq.files = "my_fq_folder")
} # }