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

Daniyar Karabayev, Askhat Molkenov, Kaiyrgali Yerulanuly, Ilyas Kabimoldayev, Asset Z. Daniyarov, Aigul Sharip, Ainur Ashenova, Zhaxybay Sh. Zhumadilov, Ulykbek Kairov

PeerJ, 2021

Full text Open access: Gold Metadata (CSL-JSON)
DOI 10.7717/peerj.11333
Data confidence 85 high
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Abstract

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).