NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

TLDR

Next‑generation sequencing generates vast amounts of data, making rigorous quality control essential and demanding fast, efficient tools for downstream analysis. Implemented in Perl, the toolkit offers user‑friendly QC utilities for Roche 454 and Illumina data, along with format conversion, trimming, and statistical analysis tools, all configurable via user‑defined parameters. The open‑source NGS QC Toolkit, freely available online, is expected to improve NGS data quality assessment and support more reliable downstream analyses.

Abstract

Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.