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

Daniyar Karabayev; Askhat Molkenov; Kaiyrgali Yerulanuly; Ilyas Kabimoldayev; Asset Daniyarov; Aigul Sharip; Ainur Seisenova; Zhaxybay Zhumadilov; Ulykbek Kairov

doi:10.7717/peerj.11333

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

PeerJ. 2021 May 3:9:e11333. doi: 10.7717/peerj.11333. eCollection 2021.

Authors

Affiliations

¹ Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
² L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan.
³ School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan.

^# Contributed equally.

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).

Keywords: Bioinformatics; Genome analysis; Genomics; Genomics data mining; NGS data analysis; VCF; Variant call format.

Grants and funding

This work has been supported by grant projects (AP08855353, AP05135430 and AP05136106) and program-targeted funding (PTF No. BR05236508) from the Committee of Science, Ministry of Education and Science of the Republic of Kazakhstan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.