fastq_quality_check

The fastqcr package allow to check fastq quality and build reports about multiple fastq files. We also present here how to plot base quality using the Rsearch package.

Load the necessary packages

library(fastqcr)
library(MiscMetabar)

## Loading required package: phyloseq

## Loading required package: ggplot2

## Loading required package: dada2

## Loading required package: Rcpp

## Loading required package: dplyr

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

## Loading required package: purrr

Install the latest version of FastQC tool on Unix systems (MAC OSX and Linux)

fastqc_install()

Run the analysis

qc.dir <- "fastqc_results"

# Demo QC directory containing zipped FASTQC reports
fastq_dir <- list_fastq_files(system.file("/extdata", package = "MiscMetabar"))
fastqcr::fastqc(dirname(fastq_dir[[1]]), qc.dir = qc.dir)
qc <- fastqcr::qc_aggregate(qc.dir)

fastqcr::qc_problems(qc)
fastqcr::qc_stats(qc)
summary(qc)

Plot base quality with Rsearch package

library(Rsearch)

fastq_dir <- list_fastq_files(system.file("/extdata", package = "MiscMetabar"))

qual_plots <- plot_base_quality(
  fastq_input = fastq_dir$fnfs,
  reverse = fastq_dir$reverse
)
print(qual_plots)

Build reports

# Building Multi QC Reports
fastqcr::qc_report(qc.dir, result.file = "multi-qc-report")

# Building One-Sample QC Reports (+ Interpretation)
qc.file <- system.file("fastqc_results", "S1_fastqc.zip", package = "fastqcr")
fastqcr::qc_report(qc.file, result.file = "one-sample-report", interpret = TRUE)