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Bug#1005356: ITP: rockhopper -- system for analyzing bacterial RNA-seq data

Package: wnpp
Severity: wishlist
Owner: Debian-med team <debian-med@lists.debian.org>
X-Debbugs-Cc: debian-devel@lists.debian.org, debian-med@lists.debian.org

* Package name    : rockhopper
  Version         : 2.0.3
  Upstream Author : Brian Tjaden
* URL             : https://cs.wellesley.edu/~btjaden/Rockhopper
* License         : GPL-3+
  Programming Lang: Java
  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

The package will be team-maintained by Debian-med team.

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