ngsReports

An R Package for managing FastQC reports and other NGS related log files inside R. Except for some periodic minor bug fixes, this branch is the current release which is also available from the Bioconductor website.

Installation

To install required packages follow the instructions below.

install.packages("BiocManager")
BiocManager::install("ngsReports")
library(ngsReports)

Usage

The paper for the package can be found here. For a detailed usage guide please see here.

ShinyApp

A Graphical User Interface (Shiny App) has been developed for interactive inspection of many FastQC reports. The ngsReports shiny app can be installed here.

Tools Supported (By Category)

Quality control

  • FastQC
  • fastp

Adapter removal and trimming

  • AdapterRemoval
  • cutadapt
  • trimmomatic
  • fastp

Deduplication

  • umi_tools dedup

Mapping and alignment

  • bowtie
  • bowtie2
  • hisat2
  • macs2 callpeak
  • picard MarkDuplicates
  • RNA-SeQC2
  • samtools flagstat
  • salmon
  • STAR

Transcript/gene quantificaiton

  • feature counts (Subread)

Genome assembly

  • BUSCO
  • quast

Citation

Please cite our paper:

@article{ward2018ngsreports,
    author = {Ward, Christopher M and To, Thu-Hien and Pederson, Stephen M},
    title = "{ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files}",
    journal = {Bioinformatics},
    year = {2019},
    month = {12},
    doi = {10.1093/bioinformatics/btz937},
    url = {https://doi.org/10.1093/bioinformatics/btz937}
}