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


  • Use of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various quality control steps separately, availability of an integrated tool that can allow one-step, automated quality control analysis of HTS datasets will significantly enhance handling large number of samples parallelly. Here, we developed HTSQualC, a stand-alone, flexible, and easy-to-use software for one-step quality control analysis of raw HTS data. HTSQualC can evaluate HTS data quality and perform filtering and trimming analysis in a single run. We evaluated the performance of HTSQualC for conducting batch analysis of HTS datasets with 322 samples with an average~1M (paired end) sequence reads per sample. HTSQualC accomplished the QC analysis in~3h in distributed mode and~31h in shared mode, thus underscoring its utility and robust performance. In addition to command-line execution, we integrated HTSQualC into the free, open-source, CyVerse cyberinfrastructure resource as a GUI interface, for wider access to experimental biologists who have limited computational resources and/or programming abilities.

published proceedings

  • Sci Rep

author list (cited authors)

  • Bedre, R., Avila, C., & Mandadi, K.

citation count

  • 2

complete list of authors

  • Bedre, Renesh||Avila, Carlos||Mandadi, Kranthi

publication date

  • January 2021