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bioRxiv · 10.1101/2020.07.23.214536

HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis

Bedre, R. H.·Avila, C. A.·Mandadi, K.
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Abstract

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 [~]3 hours in distributed mode and [~]31 hours 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.

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Bedre, R. H., Avila, C. A., Mandadi, K.. 2020-07-24. HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis. https://doi.org/10.1101/2020.07.23.214536

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