TY - JOUR T1 - Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment JF - bioRxiv DO - 10.1101/2021.04.23.441097 SP - 2021.04.23.441097 AU - Anish M.S. Shrestha AU - Joyce Emlyn B. Guiao AU - Kyle Christian R. Santiago Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/04/23/2021.04.23.441097.abstract N2 - RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. Conventional differential expression analysis for organisms without reference sequences requires performing computationally expensive and error-prone de-novo transcriptome assembly, followed by homology search against a high-confidence protein database for functional annotation. We propose a shortcut, where we obtain counts for differential expression analysis by directly aligning RNA-seq reads to the protein database. Through experiments on simulated and real data, we show drastic reductions in run-time and memory usage, with no loss in accuracy. A Snakemake implementation of our workflow is available at: https://bitbucket.org/project_samar/samarCompeting Interest StatementThe authors have declared no competing interest. ER -