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

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-alon...

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Autores principales:	Renesh Bedre, Carlos Avila, Kranthi Mandadi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/48be14bf19c34941b0978227b7eaa5ae
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spelling	oai:doaj.org-article:48be14bf19c34941b0978227b7eaa5ae2021-12-02T18:13:45ZHTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis10.1038/s41598-021-98124-32045-2322https://doaj.org/article/48be14bf19c34941b0978227b7eaa5ae2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98124-3https://doaj.org/toc/2045-2322Abstract 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 ~ 1 M (paired end) sequence reads per sample. HTSQualC accomplished the QC analysis in ~ 3 h in distributed mode and ~ 31 h 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.Renesh BedreCarlos AvilaKranthi MandadiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-7 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Renesh Bedre Carlos Avila Kranthi Mandadi HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis
description	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 ~ 1 M (paired end) sequence reads per sample. HTSQualC accomplished the QC analysis in ~ 3 h in distributed mode and ~ 31 h 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.
format	article
author	Renesh Bedre Carlos Avila Kranthi Mandadi
author_facet	Renesh Bedre Carlos Avila Kranthi Mandadi
author_sort	Renesh Bedre
title	HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis
title_short	HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis
title_full	HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis
title_fullStr	HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis
title_full_unstemmed	HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis
title_sort	htsqualc is a flexible and one-step quality control software for high-throughput sequencing data analysis
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/48be14bf19c34941b0978227b7eaa5ae
work_keys_str_mv	AT reneshbedre htsqualcisaflexibleandonestepqualitycontrolsoftwareforhighthroughputsequencingdataanalysis AT carlosavila htsqualcisaflexibleandonestepqualitycontrolsoftwareforhighthroughputsequencingdataanalysis AT kranthimandadi htsqualcisaflexibleandonestepqualitycontrolsoftwareforhighthroughputsequencingdataanalysis
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HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis

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