In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

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

Load the necessary packages

library(fastqcr)
library(MiscMetabar)

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

#| eval: false
fastqc_install()

Run the analysis

#| eval: false
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)

#| eval: false
fastqcr::qc_problems(qc)
fastqcr::qc_stats(qc)
summary(qc)

Build reports

#| eval: false
# 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)