De novo transcriptome assembly is a powerful technique in the study of non-model organisms when the reference genome is not available. However, transcriptomics data analysis often presents significant challenges due to the vast amounts of data and the common difficulties faced when removing contaminants, identifying, and annotating transcripts, and using assembled transcripts in downstream analysis. Among different programs and packages suggested for de novo assembly (Oases, Trans-ABySS, SOAPdenovo-Trans, and IDBA-Tran), the most popular is the Trinity package.

In this presentation, I describe the use of the Trinity platform for de novo transcriptome assembly and the differential gene expression pipeline integrated into Trinity software.