OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data  

作　　者：Ben-Ben Miao Wei Dong Yi-Xin Gu Zhao-Fang Han Xuan Luo Cai-Huan Ke Wei-Wei You 

机构地区：[1]State Key Laboratory of Marine Environmental Science,College of Ocean and Earth Sciences,Xiamen University,Xiamen 361102,Fujian,China [2]Hospital of Stomatology,Guanghua School of Stomatology,Guangdong Provincial Key Laboratory of Stomatology,Sun Yat-Sen University,Guangzhou 510055,Guangdong,China [3]College of Fisheries,Guangdong Ocean University,Zhanjiang 524088,Guangdong,China [4]Fujian Institute for Sustainable Oceans,Xiamen University,Xiamen 361102,Fujian,China

出　　处：《Horticulture Research》2023年第11期13-26,共14页园艺研究（英文）

基　　金：supported by grants from National Natural Science Foundation of China(32102775);Hainan Province Science and Technology Special Fund(ZDYF2022XDNY234);Earmarked Fund for CARS(No.CARS-49)and Fundamental Research Funds for the Central Universities(2072022).

摘　　要：With the advancements in high-throughput sequencing technologies such as Illumina,PacBio,and 10X Genomics platforms,and gas/liquid chromatography-mass spectrometry,large volumes of biological data in multiple formats can now be obtained through multi-omics analysis.Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems;however,it is challenging for most experimental biologists to analyse data using command-line interfaces,coding,and scripting.Based on experience with multi-omics,we have developed OmicsSuite,a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization.The suite has 175 sub-applications in 12 categories,including Sequence,Statistics,Algorithm,Genomics,Transcriptomics,Enrichment,Proteomics,Metabolomics,Clinical,Microorganism,Single Cell,and Table Operation.We created the user interface with Sequence View,Table View,and intelligent components based on JavaFX and the popular Shiny framework.The multi-omics analysis functions were developed based on BioJava and 300+packages provided by the R CRAN and Bioconductor communities,and it encompasses over 3000 adjustable parameter interfaces.OmicsSuite can directly read multi-omics raw data in FastA,FastQ,Mutation Annotation Format,mzML,Matrix,and HDF5 formats,and the programs emphasize data transfer directions and pipeline analysis functions.OmicsSuite can produce pre-publication images and tables,allowing users to focus on biological aspects.OmicsSuite offersmulti-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants.It enables researchers to freely explore the molecular information contained in multi-omics big data(Source:https://github.com/OmicsSuite/,Website:https://omicssuite.github.io,v1.3.9).

关 键 词：BREAKTHROUGH TABLES SEEKING 

分 类 号：TP39[自动化与计算机技术—计算机应用技术]