Introduction

De novo transcriptome analysis involves assembling cDNA sequences together—without the aid of a reference sequence—and then analyzing the resulting transcriptome. This technique is frequently used to study non-model organisms but is also valuable for organisms whose genome is known.

In the first part of this ebook, we discuss some reasons for doing de novo transcriptome analysis, explain the steps involved, and point out some of the challenges commonly encountered. In the second part, we explore some of the solutions available for addressing those challenges. Finally, the third part of this ebook expands upon the findings of an independent study that compares multiple professional-grade de novo transcriptome assembly packages, including Lasergene Genomics.

Our recommendations are based on extensive testing using a variety of transcriptome data sets from the NCBI Short Read Archive, as well as years of experience working with DNASTAR customers on transcriptome assembly and annotation projects.

Whether you are experienced with transcriptome analysis or thinking about trying it for the first time, this ebook will help you learn about important considerations to keep in mind throughout the process.