再搜索者：用于简化VCF文件基因组学数据挖掘的基于图形用户界面的生物信息学工具。

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

作者信息

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

机构信息

Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.

L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan.

出版信息

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

DOI:10.7717/peerj.11333

PMID:33987016

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8101456/

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).

摘要

背景

高通量测序平台生成了大量可供分析的高维基因组数据集。在测序数据分析过程中，用于分析和解释基因组数据的现代且用户友好的生物信息学工具变得至关重要。已经开发了不同的标准数据类型和文件格式来存储和分析序列及基因组数据。变异调用格式（VCF）是最广泛使用的基因组文件类型和标准格式，包含已测序样本的基因组信息和变异。

结果

现有的处理VCF文件的工具通常没有直观的图形界面，只有命令行界面，这对于对基因组数据分析感兴趣的更广泛生物医学社区来说可能具有挑战性。re-Searcher通过分块预处理VCF文件来解决这个问题，从而不占用计算机的内存。该工具既可以作为独立的用户友好型多平台图形用户界面应用程序，也可以作为网络应用程序（https://nla-lbsb.nu.edu.kz）使用。该软件包括源代码以及经过测试的VCF文件和其他信息，可在GitHub仓库（https://github.com/LabBandSB/re-Searcher）上公开获取。