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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis.

Renesh Bedre¹, Carlos Avila², Kranthi Mandadi^3,4

¹Texas A&M AgriLife Research and Extension Center, Texas A&M University, Weslaco, TX, USA.

Scientific Reports

|September 22, 2021

Summary

High-throughput sequencing (HTS) quality control is streamlined with HTSQualC, an automated software for artifact removal and data filtering. This tool enhances bioinformatics analysis efficiency for large HTS datasets.

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Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

High-throughput sequencing (HTS) is crucial in life sciences, but raw data requires artifact removal for accurate analysis.
Existing tools often perform quality control steps separately, hindering efficient processing of large sample numbers.

Purpose of the Study:

To develop an integrated, automated software solution for one-step quality control of raw HTS data.
To enhance the efficiency and accessibility of HTS data preprocessing for researchers.

Main Methods:

Development of HTSQualC, a stand-alone software for automated quality control, filtering, and trimming of HTS data.
Evaluation of HTSQualC's performance on a batch analysis of 322 HTS datasets.
Integration of HTSQualC with the CyVerse cyberinfrastructure to provide a graphical user interface (GUI).

Main Results:

HTSQualC successfully performed quality control, filtering, and trimming in a single run.
The software demonstrated robust performance, completing analysis of 322 samples efficiently (approx. 3 hours in distributed mode).
The GUI integration on CyVerse expands accessibility for biologists with limited computational expertise.

Conclusions:

HTSQualC provides a flexible, user-friendly, and efficient solution for HTS data quality control.
The software significantly improves the handling of large-scale HTS datasets.
HTSQualC democratizes HTS data analysis by offering an accessible GUI on a widely available platform.