DNASTAR Lasergene: An Integrated Package for de novo Transcriptome and RNA-Seq Analysis on a Desktop Computer

DNASTAR offers an integrated suite of software for analyzing next-gen sequencing data for a multitude of workflows and technologies, including de novo transcriptome assembly and RNA-Seq alignment. In this example, we show how both types of projects can be accomplished using the DNASTAR platform.

For de novo transcriptome projects, the first step is assembly followed by visualization. DNASTAR’s analysis tools allow users to see coverage for each assembled transcript and view the sequence alignment and variations simultaneously. Furthermore, the software is integrated with NCBI’s BLAST search, automating the process of identifying and annotating transcripts with mRNA features from closely related organisms.

In the case of RNA-Seq data, the same assembly software is used to align reads from multiple samples to DNASTAR’s curated genome template package, creating a single assembly file with annotations from GenBank, dbSNP, and COSMIC and scores from the GERP database. Again, the software can be used to visualize coverage, read alignment, and SNPs for each sample.  Furthermore, the DNASTAR software performs normalization and gene quantification based on the multi-sample alignment, allowing users to assess gene expression without additional alignment steps.  From here, users can identify genes of interest based on expression values and gene ontology information, and then view the alignment at those genes using a single project.

The integration of all these tools into a single package allows researchers to move quickly from raw data to meaningful results without the need to learn multiple bioinformatics tools.