De novo assembly of bacterial transcriptomes from RNA-seq data

A number of mature computational tools exist for both reference-based transcriptome assembly and de novo transcriptome assembly. However, most of the aforementioned tools were designed primarily for eukaryotic transcriptomes. Bacterial transcriptome assembly faces different challenges than eukaryotic transcriptome assembly. For example, bacterial genomes are generally denser than eukaryotic genomes and neighboring bacterial transcripts frequently overlap, making it challenging to distinguish the boundaries of neighboring bacterial transcripts. Polycistronic messages further complicate bacterial transcriptome assembly, particularly when different promoters of an operon are employed under different conditions. Also, models for noncoding RNAs in eukaryotes are generally inappropriate for the small regulatory RNAs common in bacteria.

In an attempt to address the paucity of computational methods for assembling bacterial transcriptomes from RNA-seq data, researchers from Wellesley College previously developed Rockhopper, a system that supports reference-based assembly of bacterial transcriptomes. In the current study, the researchers have developed novel algorithms for de novo assembly of bacterial transcriptomes, which we have implemented in the system Rockhopper 2. They show that their algorithms for de novo assembly of bacterial transcriptomes outperform other leading approaches, both in terms of sensitivity and specificity. Further, these algorithms offer dramatic improvements in efficiency, so that the de novo assembly is comparable to reference-based assembly in terms of execution time. While many de novo assemblers require high-performance computing platforms, Rockhopper 2 has been designed with limited resource requirements so that it performs effectively on common laptop machines. In addition to de novo transcriptome assembly, Rockhopper 2 is a comprehensive system that supports the various stages of RNA-seq data analysis, including normalizing data from different experiments, quantifying transcript abundance, and testing for differential transcript expression. Finally, the researchers developed Rockhopper 2 with user-friendliness in mind, so that it would be accessible to a broad range of scientists that use bacterial RNA-seq experiments in their investigations.


Availability – Rockhopper 2 is available at

Tjaden B. (2015) De novo assembly of bacterial transcriptomes from RNA-seq data. Genome Biol 16(1):1. [abstract]

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