Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ, QSEQ, FASTA, SAM, or BAM files). Rockhopper supports the following tasks:

* Reference based transcript assembly (when one or more reference genomes are available) - Aligning reads to genomes - Assembling transcripts - Identifying transcript boundaries and novel transcripts such as small RNAs * De novo transcript assembly (when reference genomes are unavailable) * Normalizing data from different experiments * Quantifying transcript abundance * Testing for differential gene expression * Characterizing operon structures * Visualizing results in a genome browser