Fastq quality check

The fastqcr package allow to check fastq quality and build reports about multiple fastq files.

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)

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)