Re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files

Karabayev D. Molkenov A. Yerulanuly K. Kabimoldayev I. Daniyarov A. Sharip A. Seisenova A. Zhumadilov Z. Kairov U.
May 2021 PeerJ Inc.

PeerJ
2021 #9

Background. High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples. Results. Existing tools for processing VCF files don’t usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher). Copyright 2021 Karabayev et al.

Bioinformatics , Genome analysis , Genomics , Genomics data mining , NGS data analysis , Variant call format , VCF

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Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan
School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan

Laboratory of Bioinformatics and Systems Biology
L.N. Gumilyov Eurasian National University
School of Medicine

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