GAMUT: A genomics big data management tool
GAMUT: A genomics big data management tool
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GAMUT：基因组学大数据管理工具
DOI：
10.1007/s12038-021-00213-y
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发表时间：
2021
影响因子：
2.9
通讯作者：
Ramakrishnan E
中科院分区：
文献类型：
--
作者：
Ramakrishnan E
对基因组样本的单核苷酸多态(SNPs)的有效分析有助于破译基因和表型之间的关系。SNP比较背后的核心原则是得出一个可能的变异列表，可以区分两组数据(总体)。这类SNP在阵列设计、基因推定和感兴趣区域的变异编目中有直接应用。我们已经开发了GAMUT(基因组学大数据管理工具)，这是一个基于大数据的解决方案，用于在考虑用户定义的分裂的情况下，基于属于不同种群的样本的划分，在大数据集中高效地运行时比较SNP。该工具基于客户端-服务器架构，以MongoDB为后端，以PrimeFaces为前端的JSF。它可以很容易地部署在Wild-Fly服务器上以及码头容器上。基于Spark的并行数据上传器可实现最佳加载时间。色域允许使用基于文本、基于染色体位置以及基于基因名称的选项对由多个样本组成的大型数据集进行动态查询。各种图表选项，如条形图和饼图以及表格格式，都可用于简化对查询数据的分析。与全基因组SNP的比较有关的结果数据也可以以不同的格式下载，如文本、html、json，用于进一步的独立分析。色域可在以下网站下载：https://github.com/bioinformatics-cdac/gamut
Efficient analysis of Single Nucleotide Polymorphisms (SNPs) across genomic samples enable in deciphering the relationship between genotype and phenotype. The core principle behind SNP comparison is to arrive at a probable list of variants that can differentiate two sets of data (populations). Such SNPs have direct applications in array design, genotype imputation and in cataloging of variants in regions of interest. We have developed GAMUT (Genomics bigdAta Management Tool), a big data-based solution for efficient run-time comparison of SNPs across large datasets based on partition of samples belonging to different populations taking into account user-defined splits. The tool is based on client-server architecture with MongoDB at the back-end and JSF with PrimeFaces as the front-end. It is readily deployable on wild-fly server as well as a docker container. Spark-based parallel data uploader enables optimal loading times. GAMUT enables dynamic querying of the large datasets consisting of multiple samples using text-based, chromosome position-based as well as gene-name based options. Various charting options like bar and pie charts along with tabular formats are available to ease the analysis of the queried data. The resultant data pertaining to comparison of genome-wide SNPs can also be downloaded in different formats like text, html, json for further stand-alone analysis. GAMUT is available for download at: https://github.com/bioinformatics-cdac/gamut
thesnppit-A高性能数据库系统用于管理大型SNP数据。
影响因子：
3.7
作者：
Groeneveld E;Lichtenberg H
通讯作者：
Lichtenberg H
影响因子：
2.7
作者：
Karabayev D;Molkenov A;Yerulanuly K;Kabimoldayev I;Daniyarov A;Sharip A;Seisenova A;Zhumadilov Z;Kairov U
通讯作者：
Kairov U