A unified platform for RNA-seq analysis in non-model species

Abstract The increasing application of RNA-seq to study non-model organisms demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights from large datasets. Here, we present a unified software suite for processing, analyzing, and interpreting RNA-seq data from any eukaryotic species. This suite consists of a) EcoOmicsDB (www.ecoomicsdb.ca), a database for ortholog mapping and cross-species comparison; b) EcoOmicsAnalyst (www.ecoomicsanalyst.ca), a platform for raw data processing and annotation; and c) ExpressAnalyst (www.expressanalyst.ca), a platform for statistical and functional analysis. The utilities of this suite are demonstrated through case studies of RNA-seq data from multiple non-model species with or without reference transcriptomes. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, the tool suite enables researchers to obtain global expression profiles and gene-level insights from raw RNA-seq reads within 24 hours.