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("steveped/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
Adapter removal and trimming
- AdapterRemoval
- cutadapt
- trimmomatic
Mapping and alignment
- bowtie
- bowtie2
- hisat2
- macs2 callpeak
- picard MarkDuplicates
- samtools flagstat
- 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}
}