Structure-profiling Experiment Quality Analyzer (SEQualyzer) Software
Visualization and quality control of high-throughput sequencing-based structure profiling data
Software described in the manuscript SEQualyzer: Interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data is available for download.
The SEQualyzer (Structure-profiling Experiment Quality Analyzer ) platform allows users to visualize and quality control data from a wide range of structure profiling experiments. The user uploads a dataset containing read stop/mutation counts and local coverages (optional) from sequencing-based profiling experiments at each residue for one to few transcripts or a transcriptome. These counts are converted into reactivity scores using a reconstruction scheme chosen by the user. The quality and variability of these scores are then evaluated using several quantitative and visual metrics. Code for SEQualyzer is written in R Shiny interactive application framework and can be downloaded along with a user manual and sample datasets.
K. Choudhary, L. Ruan, F. Deng, N. P. Shih, and S. Aviran. SEQualyzer: Interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data (in press). Bioinformatics, page btw627.
A standalone version of SEQualyzer is available for Windows users. Download link:
Another version of SEQualyzer can be used by both Mac OS and Windows users. For Mac OS users, this version provides an option to deploy SEQualyzer from desktop. Windows users may want to use this version to save disk space as the standalone version is ~200MB larger. Download link:
Refer to the user manual for instructions on input format and interpretations of output results. Note that users must install R 3.2.2 or higher to use SEQualyzer.