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

Research output: Contribution to journalArticlepeer-review

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).

Original languageEnglish
Article numbere11333
JournalPeerJ
Volume9
DOIs
Publication statusPublished - May 2021

Keywords

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

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Fingerprint

Dive into the research topics of 'Re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files'. Together they form a unique fingerprint.

Cite this