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

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).