File: rockhopper.md

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---
name: Rockhopper
url: https://cs.wellesley.edu/~btjaden/Rockhopper/index.html
description: >
  Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data.
---

Rockhopper aligns reads to coding sequences, rRNAs, tRNAs, and miscellaneous RNAs on both the sense and anti-sense strand. These statistics are summarized in the Rockhopper bar plot in this module.