system for analyzing bacterial RNA-seq data

 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