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bioRxiv · 10.1101/323535

Next-generation Sequence-analysis Toolkit (NeST): A standardized bioinformatics framework for analyzing Single Nucleotide Polymorphisms in next-generation sequencing data

Ravishankar, S.·Schmedes, S. E.·Patel, D. S.·Plucinski, M.·Talundzic, E.·Udhayakumar, V.·Vannberg, F.
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Abstract

Rapid advancements in next-generation sequencing (NGS) technologies have led to the development of numerous bioinformatics tools and pipelines. As these tools vary in their output function and complexity and some are not well-standardized, it is harder to choose a suitable pipeline to identify variants in NGS data. Here, we present NeST (NGS-analysis Toolkit), a modular consensus-based variant calling framework. NeST uses a combination of variant callers to overcome potential biases of an individual method used alone. NeST consists of four modules, that integrate open-source bioinformatics tools, a custom Variant Calling Format (VCF) parser and a summarization utility, that generate high-quality consensus variant calls. NeST was validated using targeted-amplicon deep sequencing data from 245 Plasmodium falciparum isolates to identify single-nucleotide polymorphisms conferring drug resistance. The results were verified using Sanger sequencing data for the same dataset in a supporting publication [28]. NeST offers a user-friendly pipeline for variant calling with standardized outputs and minimal computational demands for easy deployment for use with various organisms and applications.

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Ravishankar, S., Schmedes, S. E., Patel, D. S., Plucinski, M., Talundzic, E., Udhayakumar, V., Vannberg, F.. 2018-05-16. Next-generation Sequence-analysis Toolkit (NeST): A standardized bioinformatics framework for analyzing Single Nucleotide Polymorphisms in next-generation sequencing data. https://doi.org/10.1101/323535

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