GWASTool: A web pipeline for detecting SNP-phenotype associations

IF 6.2 3区综合性期刊 Q1 Multidisciplinary Fundamental Research Pub Date : 2024-07-01 DOI:10.1016/j.fmre.2024.03.005

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Abstract

The genome-wide association study (GWAS) aims to detect associations between individual single nucleotide polymorphisms (SNPs) or SNP interactions and phenotypes to decipher the genetic mechanism. Existing GWAS analysis tools have different focuses and advantages, but suffer a series of tedious and heterogeneous configurations for computation. It is inconvenient for researchers to simply choose and apply these tools, statistically and biologically analyze their results for different usages. To address these issues, we develop a user friendly web pipeline GWASTool for detecting associations, which includes simulation data generation, associated loci detection, result visualization, analysis and comparison. GWASTool provides a unified and plugin-able framework to encapsulate the heterogeneity of GWAS algorithms, simplifies the analysis steps and energizes GWAS tasks. GWASTool is implemented in Java and is freely available for public use at http://www.sdu-idea.cn/GWASTool. The website hosts a comprehensive collection of resources, including a user manual, description of integrated algorithms, data examples and standalone version for download.

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GWASTool：检测 SNP 与表型关联的网络管道

全基因组关联研究（GWAS）旨在检测单个单核苷酸多态性（SNP）或SNP相互作用与表型之间的关联，从而破译遗传机制。现有的 GWAS 分析工具各有侧重和优势，但在计算过程中存在一系列繁琐和异构的问题。研究人员不方便简单地选择和应用这些工具，并针对不同用途对其结果进行统计和生物分析。为了解决这些问题，我们开发了一个用户友好型网络管道 GWASTool，用于检测关联，包括模拟数据生成、关联基因座检测、结果可视化、分析和比较。GWASTool 提供了一个统一的、可插件化的框架，以封装 GWAS 算法的异质性，简化分析步骤，并为 GWAS 任务注入活力。GWASTool 采用 Java 实现，可在 http://www.sdu-idea.cn/GWASTool 免费供公众使用。该网站提供全面的资源，包括用户手册、集成算法说明、数据示例和供下载的独立版本。

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