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.
Highlights
Generation sequencing (NGS) technologies provide a revolutionary tool for numerous applications and are capable to generate several gigabases of sequence data in a single experimental run
quality control (QC) tools for Illumina and Roche 454 sequencing data IlluQC and 454QC tools have been developed for QC of sequencing data generated from Roche 454 and Illumina platforms, respectively
QC reports for unfiltered and filtered data are generated in different formats along with filtered HQ data files as output
Summary
Generation sequencing (NGS) technologies provide a revolutionary tool for numerous applications and are capable to generate several gigabases of sequence data in a single experimental run. 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). Most of the programs available for downstream analyses do not provide the utility for quality check and filtering of NGS data before processing.
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