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

PeerJ

article

Daniyar Karabayev¹  Askhat Molkenov¹  Kaiyrgali Yerulanuly¹  Ilyas Kabimoldayev¹  Asset Daniyarov¹  Aigul Sharip¹  Ainur Ashenova¹  Zhaxybay Zhumadilov¹  Ulykbek Kairov¹ 

[1] Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University;L.N. Gumilyov Eurasian National University;School of Medicine, Nazarbayev University

关键词: Genome analysis;    Genomics;    Bioinformatics;    Genomics data mining;    NGS data analysis;    Variant call format;    VCF;   

DOI  :  10.7717/peerj.11333

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundHigh-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.ResultsExisting 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).

【 授权许可】

CC BY