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

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 stan...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) CA), 2021-05, Vol.9, p.e11333-e11333, Article e11333
Main Authors: Karabayev, Daniyar, Molkenov, Askhat, Yerulanuly, Kaiyrgali, Kabimoldayev, Ilyas, Daniyarov, Asset, Sharip, Aigul, Seisenova, Ainur, Zhumadilov, Zhaxybay, Kairov, Ulykbek
Format: Article
Language:English
Subjects:
Bioinformatics
Computational biology
Computer graphics
Data mining
Data processing
Genetics
Genome analysis
Genomics
Genomics data mining
Genotype & phenotype
Java
Keywords
Linux
Medical Genetics
Molecular Biology
Next-generation sequencing
NGS data analysis
Software
User interface
User needs
Variant call format
Web browsers
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Summary: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. 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).
ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.11333