Package: rockhopper
Version: 2.0.3+dfsg2-4
Architecture: all
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 653
Depends: igv, default-jre
Section: science
Priority: optional
Homepage: https://cs.wellesley.edu/~btjaden/Rockhopper/
Description: 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
