RT Journal Article
SR Electronic
T1 ngsReports: An R Package for managing FastQC reports and other NGS related log files
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 313148
DO 10.1101/313148
A1 Christopher M. Ward
A1 Hein To
A1 Stephen M Pederson
YR 2018
UL http://biorxiv.org/content/early/2018/05/02/313148.abstract
AB Motivation High throughput next generation sequencing (NGS) has become exceedingly cheap facilitating studies to be undertaken containing large sample numbers. Quality control (QC) is an essential stage during analytic pipelines and can be found in the outputs of popular bioinformatics tools such as FastQC and Picard. Although these tools provide considerable power when carrying out QC, large sample numbers can make identification of systemic bias a challenge.Results We present ngsReports, an R package designed for the management and visualization of NGS reports from within an R environment. The available methods allow direct import into R of FastQC output as well as that from aligners such as HISAT2, STAR and Bowtie2. Visualization can be carried out across many samples using heatmaps rendered using ggplot2 and plotly. Moreover, these can be displayed in an interactive shiny app or a HTML report. We also provide methods to assess observed GC content in an organism dependent manner for both transcriptomic and genomic datasets. Importantly, hierarchical clustering can be carried out on heatmaps with large sample sizes to quickly identify outliers and batch effects.Availability and Implementation ngsReports is available at https://github.com/UofABioinformaticsHub/ngsReports.