Rockhopper: http://cs.wellesley.edu/~btjaden/Rockhopper/
For computational analysis of 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